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snippy

4,171
Total Errors
2205
Unique Error Types
76
Affected Users

Exit Codes

Exit CodeCount
23,166
2552
1371

Destinations

DestinationCount
cyclone_small3,455
jetstream2428

All Unique Error Messages

CountError Message
58This is snippy-core 4.6.0
Show full stderrThis is snippy-core 4.6.0 Obtained from http://github.com/tseemann/snippy Enabling bundled tools for linux Found any2fasta - /usr/local/bin/any2fasta Found samtools - /usr/local/bin/samtools Found minimap2 - /usr/local/bin/minimap2 Found bedtools - /usr/local/bin/bedtools Found snp-sites - /usr/local/bin/snp-sites Saving reference FASTA: core.ref.fa This is any2fasta 0.4.2 Opening 'ref.fna' Detected FASTA format Read 2956542 lines from 'ref.fna' Wrote 702 sequences from FASTA file. Processed 1 files. Done. Loaded 702 sequences totalling 206915596 bp. Will mask 0 regions totalling 0 bp ~ 0.00% ERROR: snippy_dirs/10_24SA010_S166_L001/snps.aligned.fa has entry 'NC_024355.1' but ref.fna doesn't.
6[04:43:40] This is snippy 4.6.0
Show full stderr[04:43:40] This is snippy 4.6.0 [04:43:40] Written by Torsten Seemann [04:43:40] Obtained from https://github.com/tseemann/snippy [04:43:40] Detected operating system: linux [04:43:40] Enabling bundled linux tools. [04:43:40] Found bwa - /usr/local/bin/bwa [04:43:40] Found bcftools - /usr/local/bin/bcftools [04:43:40] Found samtools - /usr/local/bin/samtools [04:43:40] Found java - /usr/local/bin/java [04:43:40] Found snpEff - /usr/local/bin/snpEff [04:43:40] Found samclip - /usr/local/bin/samclip [04:43:40] Found seqtk - /usr/local/bin/seqtk [04:43:40] Found parallel - /usr/local/bin/parallel [04:43:40] Found freebayes - /usr/local/bin/freebayes [04:43:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:43:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:43:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:43:40] Found vcfuniq - /usr/local/bin/vcfuniq [04:43:40] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:43:40] Found gzip - /bin/gzip [04:43:40] Found vt - /usr/local/bin/vt [04:43:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:43:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:43:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:43:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:43:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:43:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:43:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:43:41] Please supply a reference FASTA/GBK/EMBL file with --reference
6[03:39:26] This is snippy 4.6.0
Show full stderr[03:39:26] This is snippy 4.6.0 [03:39:26] Written by Torsten Seemann [03:39:26] Obtained from https://github.com/tseemann/snippy [03:39:26] Detected operating system: linux [03:39:26] Enabling bundled linux tools. [03:39:26] Found bwa - /usr/local/bin/bwa [03:39:26] Found bcftools - /usr/local/bin/bcftools [03:39:26] Found samtools - /usr/local/bin/samtools [03:39:26] Found java - /usr/local/bin/java [03:39:26] Found snpEff - /usr/local/bin/snpEff [03:39:26] Found samclip - /usr/local/bin/samclip [03:39:26] Found seqtk - /usr/local/bin/seqtk [03:39:26] Found parallel - /usr/local/bin/parallel [03:39:26] Found freebayes - /usr/local/bin/freebayes [03:39:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:39:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:39:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:39:26] Found vcfuniq - /usr/local/bin/vcfuniq [03:39:26] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:39:26] Found gzip - /bin/gzip [03:39:26] Found vt - /usr/local/bin/vt [03:39:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:39:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:39:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:39:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:39:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:39:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:39:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:39:27] Please supply a reference FASTA/GBK/EMBL file with --reference
6[06:47:49] This is snippy 4.6.0
Show full stderr[06:47:49] This is snippy 4.6.0 [06:47:49] Written by Torsten Seemann [06:47:49] Obtained from https://github.com/tseemann/snippy [06:47:49] Detected operating system: linux [06:47:49] Enabling bundled linux tools. [06:47:49] Found bwa - /usr/local/bin/bwa [06:47:49] Found bcftools - /usr/local/bin/bcftools [06:47:49] Found samtools - /usr/local/bin/samtools [06:47:49] Found java - /usr/local/bin/java [06:47:49] Found snpEff - /usr/local/bin/snpEff [06:47:49] Found samclip - /usr/local/bin/samclip [06:47:49] Found seqtk - /usr/local/bin/seqtk [06:47:49] Found parallel - /usr/local/bin/parallel [06:47:49] Found freebayes - /usr/local/bin/freebayes [06:47:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:47:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:47:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:47:49] Found vcfuniq - /usr/local/bin/vcfuniq [06:47:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:47:49] Found gzip - /bin/gzip [06:47:49] Found vt - /usr/local/bin/vt [06:47:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:47:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:47:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:47:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:47:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:47:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:47:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:47:50] Please supply a reference FASTA/GBK/EMBL file with --reference
6[16:31:25] This is snippy 4.6.0
Show full stderr[16:31:25] This is snippy 4.6.0 [16:31:25] Written by Torsten Seemann [16:31:25] Obtained from https://github.com/tseemann/snippy [16:31:25] Detected operating system: linux [16:31:25] Enabling bundled linux tools. [16:31:25] Found bwa - /usr/local/bin/bwa [16:31:25] Found bcftools - /usr/local/bin/bcftools [16:31:25] Found samtools - /usr/local/bin/samtools [16:31:25] Found java - /usr/local/bin/java [16:31:25] Found snpEff - /usr/local/bin/snpEff [16:31:25] Found samclip - /usr/local/bin/samclip [16:31:25] Found seqtk - /usr/local/bin/seqtk [16:31:25] Found parallel - /usr/local/bin/parallel [16:31:25] Found freebayes - /usr/local/bin/freebayes [16:31:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [16:31:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [16:31:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [16:31:25] Found vcfuniq - /usr/local/bin/vcfuniq [16:31:25] Found vcffirstheader - /usr/local/bin/vcffirstheader [16:31:25] Found gzip - /bin/gzip [16:31:25] Found vt - /usr/local/bin/vt [16:31:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [16:31:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [16:31:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [16:31:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [16:31:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [16:31:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [16:31:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [16:31:25] Please supply a reference FASTA/GBK/EMBL file with --reference
6[19:40:12] This is snippy 4.6.0
Show full stderr[19:40:12] This is snippy 4.6.0 [19:40:12] Written by Torsten Seemann [19:40:12] Obtained from https://github.com/tseemann/snippy [19:40:12] Detected operating system: linux [19:40:12] Enabling bundled linux tools. [19:40:12] Found bwa - /usr/local/bin/bwa [19:40:12] Found bcftools - /usr/local/bin/bcftools [19:40:12] Found samtools - /usr/local/bin/samtools [19:40:12] Found java - /usr/local/bin/java [19:40:12] Found snpEff - /usr/local/bin/snpEff [19:40:12] Found samclip - /usr/local/bin/samclip [19:40:12] Found seqtk - /usr/local/bin/seqtk [19:40:12] Found parallel - /usr/local/bin/parallel [19:40:12] Found freebayes - /usr/local/bin/freebayes [19:40:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [19:40:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [19:40:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [19:40:12] Found vcfuniq - /usr/local/bin/vcfuniq [19:40:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [19:40:12] Found gzip - /bin/gzip [19:40:12] Found vt - /usr/local/bin/vt [19:40:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [19:40:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [19:40:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [19:40:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [19:40:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [19:40:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [19:40:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [19:40:13] Please supply a reference FASTA/GBK/EMBL file with --reference
6[14:44:49] This is snippy 4.6.0
Show full stderr[14:44:49] This is snippy 4.6.0 [14:44:49] Written by Torsten Seemann [14:44:49] Obtained from https://github.com/tseemann/snippy [14:44:49] Detected operating system: linux [14:44:49] Enabling bundled linux tools. [14:44:49] Found bwa - /usr/local/bin/bwa [14:44:49] Found bcftools - /usr/local/bin/bcftools [14:44:49] Found samtools - /usr/local/bin/samtools [14:44:49] Found java - /usr/local/bin/java [14:44:49] Found snpEff - /usr/local/bin/snpEff [14:44:49] Found samclip - /usr/local/bin/samclip [14:44:49] Found seqtk - /usr/local/bin/seqtk [14:44:49] Found parallel - /usr/local/bin/parallel [14:44:49] Found freebayes - /usr/local/bin/freebayes [14:44:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:44:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:44:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:44:49] Found vcfuniq - /usr/local/bin/vcfuniq [14:44:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:44:49] Found gzip - /bin/gzip [14:44:49] Found vt - /usr/local/bin/vt [14:44:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:44:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:44:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:44:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:44:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:44:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:44:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:44:50] Please supply a reference FASTA/GBK/EMBL file with --reference
5[04:37:03] This is snippy 4.6.0
Show full stderr[04:37:03] This is snippy 4.6.0 [04:37:03] Written by Torsten Seemann [04:37:03] Obtained from https://github.com/tseemann/snippy [04:37:03] Detected operating system: linux [04:37:03] Enabling bundled linux tools. [04:37:03] Found bwa - /usr/local/bin/bwa [04:37:03] Found bcftools - /usr/local/bin/bcftools [04:37:03] Found samtools - /usr/local/bin/samtools [04:37:03] Found java - /usr/local/bin/java [04:37:03] Found snpEff - /usr/local/bin/snpEff [04:37:03] Found samclip - /usr/local/bin/samclip [04:37:03] Found seqtk - /usr/local/bin/seqtk [04:37:03] Found parallel - /usr/local/bin/parallel [04:37:03] Found freebayes - /usr/local/bin/freebayes [04:37:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:37:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:37:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:37:03] Found vcfuniq - /usr/local/bin/vcfuniq [04:37:03] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:37:03] Found gzip - /bin/gzip [04:37:03] Found vt - /usr/local/bin/vt [04:37:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:37:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:37:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:37:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:37:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:37:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:37:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:37:03] Please supply a reference FASTA/GBK/EMBL file with --reference
5[04:43:55] This is snippy 4.6.0
Show full stderr[04:43:55] This is snippy 4.6.0 [04:43:55] Written by Torsten Seemann [04:43:55] Obtained from https://github.com/tseemann/snippy [04:43:55] Detected operating system: linux [04:43:55] Enabling bundled linux tools. [04:43:55] Found bwa - /usr/local/bin/bwa [04:43:55] Found bcftools - /usr/local/bin/bcftools [04:43:55] Found samtools - /usr/local/bin/samtools [04:43:55] Found java - /usr/local/bin/java [04:43:55] Found snpEff - /usr/local/bin/snpEff [04:43:55] Found samclip - /usr/local/bin/samclip [04:43:55] Found seqtk - /usr/local/bin/seqtk [04:43:55] Found parallel - /usr/local/bin/parallel [04:43:55] Found freebayes - /usr/local/bin/freebayes [04:43:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:43:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:43:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:43:55] Found vcfuniq - /usr/local/bin/vcfuniq [04:43:55] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:43:56] Found gzip - /bin/gzip [04:43:56] Found vt - /usr/local/bin/vt [04:43:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:43:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:43:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:43:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:43:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:43:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:43:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:43:56] Please supply a reference FASTA/GBK/EMBL file with --reference
5[07:25:52] This is snippy 4.6.0
Show full stderr[07:25:52] This is snippy 4.6.0 [07:25:52] Written by Torsten Seemann [07:25:52] Obtained from https://github.com/tseemann/snippy [07:25:52] Detected operating system: linux [07:25:52] Enabling bundled linux tools. [07:25:52] Found bwa - /usr/local/bin/bwa [07:25:52] Found bcftools - /usr/local/bin/bcftools [07:25:52] Found samtools - /usr/local/bin/samtools [07:25:52] Found java - /usr/local/bin/java [07:25:52] Found snpEff - /usr/local/bin/snpEff [07:25:52] Found samclip - /usr/local/bin/samclip [07:25:52] Found seqtk - /usr/local/bin/seqtk [07:25:52] Found parallel - /usr/local/bin/parallel [07:25:52] Found freebayes - /usr/local/bin/freebayes [07:25:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:25:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:25:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:25:52] Found vcfuniq - /usr/local/bin/vcfuniq [07:25:52] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:25:52] Found gzip - /bin/gzip [07:25:52] Found vt - /usr/local/bin/vt [07:25:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:25:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:25:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:25:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:25:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:25:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:25:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:25:53] Please supply a reference FASTA/GBK/EMBL file with --reference
5[07:09:59] This is snippy 4.6.0
Show full stderr[07:09:59] This is snippy 4.6.0 [07:09:59] Written by Torsten Seemann [07:09:59] Obtained from https://github.com/tseemann/snippy [07:09:59] Detected operating system: linux [07:09:59] Enabling bundled linux tools. [07:09:59] Found bwa - /usr/local/bin/bwa [07:09:59] Found bcftools - /usr/local/bin/bcftools [07:09:59] Found samtools - /usr/local/bin/samtools [07:09:59] Found java - /usr/local/bin/java [07:09:59] Found snpEff - /usr/local/bin/snpEff [07:09:59] Found samclip - /usr/local/bin/samclip [07:09:59] Found seqtk - /usr/local/bin/seqtk [07:09:59] Found parallel - /usr/local/bin/parallel [07:09:59] Found freebayes - /usr/local/bin/freebayes [07:09:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:09:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:09:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:09:59] Found vcfuniq - /usr/local/bin/vcfuniq [07:09:59] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:09:59] Found gzip - /bin/gzip [07:09:59] Found vt - /usr/local/bin/vt [07:09:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:09:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:09:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:09:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:09:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:10:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:10:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:10:00] Please supply a reference FASTA/GBK/EMBL file with --reference
5[07:14:02] This is snippy 4.6.0
Show full stderr[07:14:02] This is snippy 4.6.0 [07:14:02] Written by Torsten Seemann [07:14:02] Obtained from https://github.com/tseemann/snippy [07:14:02] Detected operating system: linux [07:14:02] Enabling bundled linux tools. [07:14:02] Found bwa - /usr/local/bin/bwa [07:14:02] Found bcftools - /usr/local/bin/bcftools [07:14:02] Found samtools - /usr/local/bin/samtools [07:14:02] Found java - /usr/local/bin/java [07:14:02] Found snpEff - /usr/local/bin/snpEff [07:14:02] Found samclip - /usr/local/bin/samclip [07:14:02] Found seqtk - /usr/local/bin/seqtk [07:14:02] Found parallel - /usr/local/bin/parallel [07:14:02] Found freebayes - /usr/local/bin/freebayes [07:14:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:14:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:14:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:14:02] Found vcfuniq - /usr/local/bin/vcfuniq [07:14:02] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:14:02] Found gzip - /bin/gzip [07:14:02] Found vt - /usr/local/bin/vt [07:14:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:14:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:14:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:14:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:14:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:14:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:14:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:14:02] Please supply a reference FASTA/GBK/EMBL file with --reference
5[09:13:01] This is snippy 4.6.0
Show full stderr[09:13:01] This is snippy 4.6.0 [09:13:01] Written by Torsten Seemann [09:13:01] Obtained from https://github.com/tseemann/snippy [09:13:01] Detected operating system: linux [09:13:01] Enabling bundled linux tools. [09:13:01] Found bwa - /usr/local/bin/bwa [09:13:01] Found bcftools - /usr/local/bin/bcftools [09:13:01] Found samtools - /usr/local/bin/samtools [09:13:01] Found java - /usr/local/bin/java [09:13:01] Found snpEff - /usr/local/bin/snpEff [09:13:01] Found samclip - /usr/local/bin/samclip [09:13:01] Found seqtk - /usr/local/bin/seqtk [09:13:01] Found parallel - /usr/local/bin/parallel [09:13:01] Found freebayes - /usr/local/bin/freebayes [09:13:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [09:13:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [09:13:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [09:13:01] Found vcfuniq - /usr/local/bin/vcfuniq [09:13:01] Found vcffirstheader - /usr/local/bin/vcffirstheader [09:13:01] Found gzip - /bin/gzip [09:13:01] Found vt - /usr/local/bin/vt [09:13:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [09:13:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [09:13:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [09:13:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [09:13:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [09:13:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [09:13:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [09:13:02] Please supply a reference FASTA/GBK/EMBL file with --reference
4[21:23:37] This is snippy 4.6.0
Show full stderr[21:23:37] This is snippy 4.6.0 [21:23:37] Written by Torsten Seemann [21:23:37] Obtained from https://github.com/tseemann/snippy [21:23:37] Detected operating system: linux [21:23:37] Enabling bundled linux tools. [21:23:37] Found bwa - /usr/local/bin/bwa [21:23:37] Found bcftools - /usr/local/bin/bcftools [21:23:37] Found samtools - /usr/local/bin/samtools [21:23:37] Found java - /usr/local/bin/java [21:23:37] Found snpEff - /usr/local/bin/snpEff [21:23:37] Found samclip - /usr/local/bin/samclip [21:23:37] Found seqtk - /usr/local/bin/seqtk [21:23:37] Found parallel - /usr/local/bin/parallel [21:23:37] Found freebayes - /usr/local/bin/freebayes [21:23:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:23:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:23:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:23:37] Found vcfuniq - /usr/local/bin/vcfuniq [21:23:37] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:23:37] Found gzip - /bin/gzip [21:23:37] Found vt - /usr/local/bin/vt [21:23:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:23:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:23:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:23:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:23:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:23:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:23:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:23:38] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat [21:23:38] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat'
4[04:36:47] This is snippy 4.6.0
Show full stderr[04:36:47] This is snippy 4.6.0 [04:36:47] Written by Torsten Seemann [04:36:47] Obtained from https://github.com/tseemann/snippy [04:36:47] Detected operating system: linux [04:36:47] Enabling bundled linux tools. [04:36:47] Found bwa - /usr/local/bin/bwa [04:36:47] Found bcftools - /usr/local/bin/bcftools [04:36:47] Found samtools - /usr/local/bin/samtools [04:36:47] Found java - /usr/local/bin/java [04:36:47] Found snpEff - /usr/local/bin/snpEff [04:36:47] Found samclip - /usr/local/bin/samclip [04:36:47] Found seqtk - /usr/local/bin/seqtk [04:36:47] Found parallel - /usr/local/bin/parallel [04:36:47] Found freebayes - /usr/local/bin/freebayes [04:36:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:36:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:36:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:36:47] Found vcfuniq - /usr/local/bin/vcfuniq [04:36:47] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:36:47] Found gzip - /bin/gzip [04:36:47] Found vt - /usr/local/bin/vt [04:36:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:36:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:36:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:36:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:36:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:36:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:36:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:36:49] Please supply a reference FASTA/GBK/EMBL file with --reference
4[04:39:09] This is snippy 4.6.0
Show full stderr[04:39:09] This is snippy 4.6.0 [04:39:09] Written by Torsten Seemann [04:39:09] Obtained from https://github.com/tseemann/snippy [04:39:09] Detected operating system: linux [04:39:09] Enabling bundled linux tools. [04:39:09] Found bwa - /usr/local/bin/bwa [04:39:09] Found bcftools - /usr/local/bin/bcftools [04:39:09] Found samtools - /usr/local/bin/samtools [04:39:09] Found java - /usr/local/bin/java [04:39:09] Found snpEff - /usr/local/bin/snpEff [04:39:09] Found samclip - /usr/local/bin/samclip [04:39:09] Found seqtk - /usr/local/bin/seqtk [04:39:09] Found parallel - /usr/local/bin/parallel [04:39:09] Found freebayes - /usr/local/bin/freebayes [04:39:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:39:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:39:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:39:09] Found vcfuniq - /usr/local/bin/vcfuniq [04:39:09] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:39:09] Found gzip - /bin/gzip [04:39:09] Found vt - /usr/local/bin/vt [04:39:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:39:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:39:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:39:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:39:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:39:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:39:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:39:10] Please supply a reference FASTA/GBK/EMBL file with --reference
4[04:38:18] This is snippy 4.6.0
Show full stderr[04:38:18] This is snippy 4.6.0 [04:38:18] Written by Torsten Seemann [04:38:18] Obtained from https://github.com/tseemann/snippy [04:38:18] Detected operating system: linux [04:38:18] Enabling bundled linux tools. [04:38:18] Found bwa - /usr/local/bin/bwa [04:38:18] Found bcftools - /usr/local/bin/bcftools [04:38:18] Found samtools - /usr/local/bin/samtools [04:38:18] Found java - /usr/local/bin/java [04:38:18] Found snpEff - /usr/local/bin/snpEff [04:38:18] Found samclip - /usr/local/bin/samclip [04:38:18] Found seqtk - /usr/local/bin/seqtk [04:38:18] Found parallel - /usr/local/bin/parallel [04:38:18] Found freebayes - /usr/local/bin/freebayes [04:38:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:38:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:38:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:38:18] Found vcfuniq - /usr/local/bin/vcfuniq [04:38:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:38:18] Found gzip - /bin/gzip [04:38:18] Found vt - /usr/local/bin/vt [04:38:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:38:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:38:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:38:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:38:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:38:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:38:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:38:19] Please supply a reference FASTA/GBK/EMBL file with --reference
4[04:42:48] This is snippy 4.6.0
Show full stderr[04:42:48] This is snippy 4.6.0 [04:42:48] Written by Torsten Seemann [04:42:48] Obtained from https://github.com/tseemann/snippy [04:42:48] Detected operating system: linux [04:42:48] Enabling bundled linux tools. [04:42:48] Found bwa - /usr/local/bin/bwa [04:42:48] Found bcftools - /usr/local/bin/bcftools [04:42:48] Found samtools - /usr/local/bin/samtools [04:42:48] Found java - /usr/local/bin/java [04:42:48] Found snpEff - /usr/local/bin/snpEff [04:42:48] Found samclip - /usr/local/bin/samclip [04:42:48] Found seqtk - /usr/local/bin/seqtk [04:42:48] Found parallel - /usr/local/bin/parallel [04:42:48] Found freebayes - /usr/local/bin/freebayes [04:42:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:42:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:42:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:42:48] Found vcfuniq - /usr/local/bin/vcfuniq [04:42:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:42:48] Found gzip - /bin/gzip [04:42:48] Found vt - /usr/local/bin/vt [04:42:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:42:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:42:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:42:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:42:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:42:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:42:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:42:49] Please supply a reference FASTA/GBK/EMBL file with --reference
4[04:54:49] This is snippy 4.6.0
Show full stderr[04:54:49] This is snippy 4.6.0 [04:54:49] Written by Torsten Seemann [04:54:49] Obtained from https://github.com/tseemann/snippy [04:54:49] Detected operating system: linux [04:54:49] Enabling bundled linux tools. [04:54:49] Found bwa - /usr/local/bin/bwa [04:54:49] Found bcftools - /usr/local/bin/bcftools [04:54:49] Found samtools - /usr/local/bin/samtools [04:54:49] Found java - /usr/local/bin/java [04:54:49] Found snpEff - /usr/local/bin/snpEff [04:54:49] Found samclip - /usr/local/bin/samclip [04:54:49] Found seqtk - /usr/local/bin/seqtk [04:54:49] Found parallel - /usr/local/bin/parallel [04:54:49] Found freebayes - /usr/local/bin/freebayes [04:54:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:54:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:54:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:54:49] Found vcfuniq - /usr/local/bin/vcfuniq [04:54:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:54:49] Found gzip - /bin/gzip [04:54:49] Found vt - /usr/local/bin/vt [04:54:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:54:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:54:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:54:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:54:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:54:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:54:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:54:50] Please supply a reference FASTA/GBK/EMBL file with --reference
4[04:56:01] This is snippy 4.6.0
Show full stderr[04:56:01] This is snippy 4.6.0 [04:56:01] Written by Torsten Seemann [04:56:01] Obtained from https://github.com/tseemann/snippy [04:56:01] Detected operating system: linux [04:56:01] Enabling bundled linux tools. [04:56:01] Found bwa - /usr/local/bin/bwa [04:56:01] Found bcftools - /usr/local/bin/bcftools [04:56:01] Found samtools - /usr/local/bin/samtools [04:56:01] Found java - /usr/local/bin/java [04:56:01] Found snpEff - /usr/local/bin/snpEff [04:56:01] Found samclip - /usr/local/bin/samclip [04:56:01] Found seqtk - /usr/local/bin/seqtk [04:56:01] Found parallel - /usr/local/bin/parallel [04:56:01] Found freebayes - /usr/local/bin/freebayes [04:56:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:56:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:56:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:56:01] Found vcfuniq - /usr/local/bin/vcfuniq [04:56:01] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:56:01] Found gzip - /bin/gzip [04:56:01] Found vt - /usr/local/bin/vt [04:56:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:56:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:56:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:56:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:56:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:56:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:56:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:56:02] Please supply a reference FASTA/GBK/EMBL file with --reference
4[04:56:15] This is snippy 4.6.0
Show full stderr[04:56:15] This is snippy 4.6.0 [04:56:15] Written by Torsten Seemann [04:56:15] Obtained from https://github.com/tseemann/snippy [04:56:15] Detected operating system: linux [04:56:15] Enabling bundled linux tools. [04:56:15] Found bwa - /usr/local/bin/bwa [04:56:15] Found bcftools - /usr/local/bin/bcftools [04:56:15] Found samtools - /usr/local/bin/samtools [04:56:15] Found java - /usr/local/bin/java [04:56:15] Found snpEff - /usr/local/bin/snpEff [04:56:15] Found samclip - /usr/local/bin/samclip [04:56:15] Found seqtk - /usr/local/bin/seqtk [04:56:15] Found parallel - /usr/local/bin/parallel [04:56:15] Found freebayes - /usr/local/bin/freebayes [04:56:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:56:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:56:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:56:15] Found vcfuniq - /usr/local/bin/vcfuniq [04:56:15] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:56:15] Found gzip - /bin/gzip [04:56:15] Found vt - /usr/local/bin/vt [04:56:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:56:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:56:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:56:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:56:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:56:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:56:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:56:16] Please supply a reference FASTA/GBK/EMBL file with --reference
4[04:56:30] This is snippy 4.6.0
Show full stderr[04:56:30] This is snippy 4.6.0 [04:56:30] Written by Torsten Seemann [04:56:30] Obtained from https://github.com/tseemann/snippy [04:56:30] Detected operating system: linux [04:56:30] Enabling bundled linux tools. [04:56:30] Found bwa - /usr/local/bin/bwa [04:56:30] Found bcftools - /usr/local/bin/bcftools [04:56:30] Found samtools - /usr/local/bin/samtools [04:56:30] Found java - /usr/local/bin/java [04:56:30] Found snpEff - /usr/local/bin/snpEff [04:56:30] Found samclip - /usr/local/bin/samclip [04:56:30] Found seqtk - /usr/local/bin/seqtk [04:56:30] Found parallel - /usr/local/bin/parallel [04:56:30] Found freebayes - /usr/local/bin/freebayes [04:56:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:56:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:56:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:56:30] Found vcfuniq - /usr/local/bin/vcfuniq [04:56:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:56:30] Found gzip - /bin/gzip [04:56:30] Found vt - /usr/local/bin/vt [04:56:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:56:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:56:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:56:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:56:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:56:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:56:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:56:31] Please supply a reference FASTA/GBK/EMBL file with --reference
4[04:58:18] This is snippy 4.6.0
Show full stderr[04:58:18] This is snippy 4.6.0 [04:58:18] Written by Torsten Seemann [04:58:18] Obtained from https://github.com/tseemann/snippy [04:58:18] Detected operating system: linux [04:58:18] Enabling bundled linux tools. [04:58:18] Found bwa - /usr/local/bin/bwa [04:58:18] Found bcftools - /usr/local/bin/bcftools [04:58:18] Found samtools - /usr/local/bin/samtools [04:58:18] Found java - /usr/local/bin/java [04:58:18] Found snpEff - /usr/local/bin/snpEff [04:58:18] Found samclip - /usr/local/bin/samclip [04:58:18] Found seqtk - /usr/local/bin/seqtk [04:58:18] Found parallel - /usr/local/bin/parallel [04:58:18] Found freebayes - /usr/local/bin/freebayes [04:58:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:58:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:58:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:58:18] Found vcfuniq - /usr/local/bin/vcfuniq [04:58:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:58:18] Found gzip - /bin/gzip [04:58:18] Found vt - /usr/local/bin/vt [04:58:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:58:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:58:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:58:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:58:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:58:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:58:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:58:19] Please supply a reference FASTA/GBK/EMBL file with --reference
4[05:02:20] This is snippy 4.6.0
Show full stderr[05:02:20] This is snippy 4.6.0 [05:02:20] Written by Torsten Seemann [05:02:20] Obtained from https://github.com/tseemann/snippy [05:02:20] Detected operating system: linux [05:02:20] Enabling bundled linux tools. [05:02:20] Found bwa - /usr/local/bin/bwa [05:02:20] Found bcftools - /usr/local/bin/bcftools [05:02:20] Found samtools - /usr/local/bin/samtools [05:02:20] Found java - /usr/local/bin/java [05:02:20] Found snpEff - /usr/local/bin/snpEff [05:02:20] Found samclip - /usr/local/bin/samclip [05:02:20] Found seqtk - /usr/local/bin/seqtk [05:02:20] Found parallel - /usr/local/bin/parallel [05:02:20] Found freebayes - /usr/local/bin/freebayes [05:02:20] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:02:20] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:02:20] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:02:20] Found vcfuniq - /usr/local/bin/vcfuniq [05:02:20] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:02:20] Found gzip - /bin/gzip [05:02:20] Found vt - /usr/local/bin/vt [05:02:20] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:02:20] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:02:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:02:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:02:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:02:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:02:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:02:21] Please supply a reference FASTA/GBK/EMBL file with --reference
4[05:02:48] This is snippy 4.6.0
Show full stderr[05:02:48] This is snippy 4.6.0 [05:02:48] Written by Torsten Seemann [05:02:48] Obtained from https://github.com/tseemann/snippy [05:02:48] Detected operating system: linux [05:02:48] Enabling bundled linux tools. [05:02:48] Found bwa - /usr/local/bin/bwa [05:02:48] Found bcftools - /usr/local/bin/bcftools [05:02:48] Found samtools - /usr/local/bin/samtools [05:02:48] Found java - /usr/local/bin/java [05:02:48] Found snpEff - /usr/local/bin/snpEff [05:02:48] Found samclip - /usr/local/bin/samclip [05:02:48] Found seqtk - /usr/local/bin/seqtk [05:02:48] Found parallel - /usr/local/bin/parallel [05:02:48] Found freebayes - /usr/local/bin/freebayes [05:02:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:02:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:02:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:02:49] Found vcfuniq - /usr/local/bin/vcfuniq [05:02:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:02:49] Found gzip - /bin/gzip [05:02:49] Found vt - /usr/local/bin/vt [05:02:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:02:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:02:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:02:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:02:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:02:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:02:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:02:49] Please supply a reference FASTA/GBK/EMBL file with --reference
4[05:05:18] This is snippy 4.6.0
Show full stderr[05:05:18] This is snippy 4.6.0 [05:05:18] Written by Torsten Seemann [05:05:18] Obtained from https://github.com/tseemann/snippy [05:05:18] Detected operating system: linux [05:05:18] Enabling bundled linux tools. [05:05:18] Found bwa - /usr/local/bin/bwa [05:05:18] Found bcftools - /usr/local/bin/bcftools [05:05:18] Found samtools - /usr/local/bin/samtools [05:05:18] Found java - /usr/local/bin/java [05:05:18] Found snpEff - /usr/local/bin/snpEff [05:05:18] Found samclip - /usr/local/bin/samclip [05:05:18] Found seqtk - /usr/local/bin/seqtk [05:05:18] Found parallel - /usr/local/bin/parallel [05:05:18] Found freebayes - /usr/local/bin/freebayes [05:05:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:05:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:05:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:05:18] Found vcfuniq - /usr/local/bin/vcfuniq [05:05:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:05:18] Found gzip - /bin/gzip [05:05:18] Found vt - /usr/local/bin/vt [05:05:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:05:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:05:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:05:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:05:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:05:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:05:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:05:19] Please supply a reference FASTA/GBK/EMBL file with --reference
4[05:06:21] This is snippy 4.6.0
Show full stderr[05:06:21] This is snippy 4.6.0 [05:06:21] Written by Torsten Seemann [05:06:21] Obtained from https://github.com/tseemann/snippy [05:06:21] Detected operating system: linux [05:06:21] Enabling bundled linux tools. [05:06:21] Found bwa - /usr/local/bin/bwa [05:06:21] Found bcftools - /usr/local/bin/bcftools [05:06:21] Found samtools - /usr/local/bin/samtools [05:06:21] Found java - /usr/local/bin/java [05:06:21] Found snpEff - /usr/local/bin/snpEff [05:06:21] Found samclip - /usr/local/bin/samclip [05:06:21] Found seqtk - /usr/local/bin/seqtk [05:06:21] Found parallel - /usr/local/bin/parallel [05:06:21] Found freebayes - /usr/local/bin/freebayes [05:06:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:06:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:06:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:06:21] Found vcfuniq - /usr/local/bin/vcfuniq [05:06:21] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:06:21] Found gzip - /bin/gzip [05:06:21] Found vt - /usr/local/bin/vt [05:06:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:06:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:06:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:06:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:06:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:06:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:06:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:06:22] Please supply a reference FASTA/GBK/EMBL file with --reference
4[05:06:36] This is snippy 4.6.0
Show full stderr[05:06:36] This is snippy 4.6.0 [05:06:36] Written by Torsten Seemann [05:06:36] Obtained from https://github.com/tseemann/snippy [05:06:36] Detected operating system: linux [05:06:36] Enabling bundled linux tools. [05:06:36] Found bwa - /usr/local/bin/bwa [05:06:36] Found bcftools - /usr/local/bin/bcftools [05:06:36] Found samtools - /usr/local/bin/samtools [05:06:36] Found java - /usr/local/bin/java [05:06:36] Found snpEff - /usr/local/bin/snpEff [05:06:36] Found samclip - /usr/local/bin/samclip [05:06:36] Found seqtk - /usr/local/bin/seqtk [05:06:36] Found parallel - /usr/local/bin/parallel [05:06:36] Found freebayes - /usr/local/bin/freebayes [05:06:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:06:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:06:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:06:36] Found vcfuniq - /usr/local/bin/vcfuniq [05:06:36] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:06:36] Found gzip - /bin/gzip [05:06:36] Found vt - /usr/local/bin/vt [05:06:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:06:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:06:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:06:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:06:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:06:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:06:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:06:37] Please supply a reference FASTA/GBK/EMBL file with --reference
4[05:06:52] This is snippy 4.6.0
Show full stderr[05:06:52] This is snippy 4.6.0 [05:06:52] Written by Torsten Seemann [05:06:52] Obtained from https://github.com/tseemann/snippy [05:06:52] Detected operating system: linux [05:06:52] Enabling bundled linux tools. [05:06:52] Found bwa - /usr/local/bin/bwa [05:06:52] Found bcftools - /usr/local/bin/bcftools [05:06:52] Found samtools - /usr/local/bin/samtools [05:06:52] Found java - /usr/local/bin/java [05:06:52] Found snpEff - /usr/local/bin/snpEff [05:06:52] Found samclip - /usr/local/bin/samclip [05:06:52] Found seqtk - /usr/local/bin/seqtk [05:06:52] Found parallel - /usr/local/bin/parallel [05:06:52] Found freebayes - /usr/local/bin/freebayes [05:06:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:06:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:06:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:06:52] Found vcfuniq - /usr/local/bin/vcfuniq [05:06:52] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:06:52] Found gzip - /bin/gzip [05:06:52] Found vt - /usr/local/bin/vt [05:06:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:06:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:06:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:06:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:06:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:06:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:06:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:06:53] Please supply a reference FASTA/GBK/EMBL file with --reference
4[03:39:40] This is snippy 4.6.0
Show full stderr[03:39:40] This is snippy 4.6.0 [03:39:40] Written by Torsten Seemann [03:39:40] Obtained from https://github.com/tseemann/snippy [03:39:40] Detected operating system: linux [03:39:40] Enabling bundled linux tools. [03:39:40] Found bwa - /usr/local/bin/bwa [03:39:40] Found bcftools - /usr/local/bin/bcftools [03:39:40] Found samtools - /usr/local/bin/samtools [03:39:40] Found java - /usr/local/bin/java [03:39:40] Found snpEff - /usr/local/bin/snpEff [03:39:40] Found samclip - /usr/local/bin/samclip [03:39:40] Found seqtk - /usr/local/bin/seqtk [03:39:40] Found parallel - /usr/local/bin/parallel [03:39:40] Found freebayes - /usr/local/bin/freebayes [03:39:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:39:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:39:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:39:40] Found vcfuniq - /usr/local/bin/vcfuniq [03:39:40] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:39:40] Found gzip - /bin/gzip [03:39:40] Found vt - /usr/local/bin/vt [03:39:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:39:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:39:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:39:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:39:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:39:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:39:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:39:41] Please supply a reference FASTA/GBK/EMBL file with --reference
4[03:39:56] This is snippy 4.6.0
Show full stderr[03:39:56] This is snippy 4.6.0 [03:39:56] Written by Torsten Seemann [03:39:56] Obtained from https://github.com/tseemann/snippy [03:39:56] Detected operating system: linux [03:39:56] Enabling bundled linux tools. [03:39:56] Found bwa - /usr/local/bin/bwa [03:39:56] Found bcftools - /usr/local/bin/bcftools [03:39:56] Found samtools - /usr/local/bin/samtools [03:39:56] Found java - /usr/local/bin/java [03:39:56] Found snpEff - /usr/local/bin/snpEff [03:39:56] Found samclip - /usr/local/bin/samclip [03:39:56] Found seqtk - /usr/local/bin/seqtk [03:39:56] Found parallel - /usr/local/bin/parallel [03:39:56] Found freebayes - /usr/local/bin/freebayes [03:39:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:39:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:39:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:39:56] Found vcfuniq - /usr/local/bin/vcfuniq [03:39:56] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:39:56] Found gzip - /bin/gzip [03:39:56] Found vt - /usr/local/bin/vt [03:39:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:39:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:39:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:39:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:39:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:39:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:39:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:39:57] Please supply a reference FASTA/GBK/EMBL file with --reference
4[03:41:42] This is snippy 4.6.0
Show full stderr[03:41:42] This is snippy 4.6.0 [03:41:42] Written by Torsten Seemann [03:41:42] Obtained from https://github.com/tseemann/snippy [03:41:42] Detected operating system: linux [03:41:42] Enabling bundled linux tools. [03:41:42] Found bwa - /usr/local/bin/bwa [03:41:42] Found bcftools - /usr/local/bin/bcftools [03:41:42] Found samtools - /usr/local/bin/samtools [03:41:42] Found java - /usr/local/bin/java [03:41:42] Found snpEff - /usr/local/bin/snpEff [03:41:42] Found samclip - /usr/local/bin/samclip [03:41:42] Found seqtk - /usr/local/bin/seqtk [03:41:42] Found parallel - /usr/local/bin/parallel [03:41:42] Found freebayes - /usr/local/bin/freebayes [03:41:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:41:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:41:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:41:42] Found vcfuniq - /usr/local/bin/vcfuniq [03:41:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:41:42] Found gzip - /bin/gzip [03:41:42] Found vt - /usr/local/bin/vt [03:41:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:41:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:41:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:41:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:41:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:41:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:41:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:41:43] Please supply a reference FASTA/GBK/EMBL file with --reference
4[03:41:57] This is snippy 4.6.0
Show full stderr[03:41:57] This is snippy 4.6.0 [03:41:57] Written by Torsten Seemann [03:41:57] Obtained from https://github.com/tseemann/snippy [03:41:57] Detected operating system: linux [03:41:57] Enabling bundled linux tools. [03:41:57] Found bwa - /usr/local/bin/bwa [03:41:57] Found bcftools - /usr/local/bin/bcftools [03:41:57] Found samtools - /usr/local/bin/samtools [03:41:57] Found java - /usr/local/bin/java [03:41:57] Found snpEff - /usr/local/bin/snpEff [03:41:57] Found samclip - /usr/local/bin/samclip [03:41:57] Found seqtk - /usr/local/bin/seqtk [03:41:57] Found parallel - /usr/local/bin/parallel [03:41:57] Found freebayes - /usr/local/bin/freebayes [03:41:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:41:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:41:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:41:57] Found vcfuniq - /usr/local/bin/vcfuniq [03:41:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:41:57] Found gzip - /bin/gzip [03:41:57] Found vt - /usr/local/bin/vt [03:41:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:41:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:41:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:41:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:41:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:41:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:41:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:41:58] Please supply a reference FASTA/GBK/EMBL file with --reference
4[03:42:35] This is snippy 4.6.0
Show full stderr[03:42:35] This is snippy 4.6.0 [03:42:35] Written by Torsten Seemann [03:42:35] Obtained from https://github.com/tseemann/snippy [03:42:35] Detected operating system: linux [03:42:35] Enabling bundled linux tools. [03:42:35] Found bwa - /usr/local/bin/bwa [03:42:35] Found bcftools - /usr/local/bin/bcftools [03:42:35] Found samtools - /usr/local/bin/samtools [03:42:35] Found java - /usr/local/bin/java [03:42:35] Found snpEff - /usr/local/bin/snpEff [03:42:35] Found samclip - /usr/local/bin/samclip [03:42:35] Found seqtk - /usr/local/bin/seqtk [03:42:35] Found parallel - /usr/local/bin/parallel [03:42:35] Found freebayes - /usr/local/bin/freebayes [03:42:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:42:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:42:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:42:35] Found vcfuniq - /usr/local/bin/vcfuniq [03:42:35] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:42:35] Found gzip - /bin/gzip [03:42:35] Found vt - /usr/local/bin/vt [03:42:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:42:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:42:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:42:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:42:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:42:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:42:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:42:36] Please supply a reference FASTA/GBK/EMBL file with --reference
4[03:42:53] This is snippy 4.6.0
Show full stderr[03:42:53] This is snippy 4.6.0 [03:42:53] Written by Torsten Seemann [03:42:53] Obtained from https://github.com/tseemann/snippy [03:42:53] Detected operating system: linux [03:42:53] Enabling bundled linux tools. [03:42:53] Found bwa - /usr/local/bin/bwa [03:42:53] Found bcftools - /usr/local/bin/bcftools [03:42:53] Found samtools - /usr/local/bin/samtools [03:42:53] Found java - /usr/local/bin/java [03:42:53] Found snpEff - /usr/local/bin/snpEff [03:42:53] Found samclip - /usr/local/bin/samclip [03:42:53] Found seqtk - /usr/local/bin/seqtk [03:42:53] Found parallel - /usr/local/bin/parallel [03:42:53] Found freebayes - /usr/local/bin/freebayes [03:42:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:42:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:42:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:42:53] Found vcfuniq - /usr/local/bin/vcfuniq [03:42:53] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:42:53] Found gzip - /bin/gzip [03:42:53] Found vt - /usr/local/bin/vt [03:42:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:42:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:42:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:42:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:42:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:42:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:42:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:42:54] Please supply a reference FASTA/GBK/EMBL file with --reference
4[05:58:56] This is snippy 4.6.0
Show full stderr[05:58:56] This is snippy 4.6.0 [05:58:56] Written by Torsten Seemann [05:58:56] Obtained from https://github.com/tseemann/snippy [05:58:56] Detected operating system: linux [05:58:56] Enabling bundled linux tools. [05:58:56] Found bwa - /usr/local/bin/bwa [05:58:56] Found bcftools - /usr/local/bin/bcftools [05:58:56] Found samtools - /usr/local/bin/samtools [05:58:56] Found java - /usr/local/bin/java [05:58:56] Found snpEff - /usr/local/bin/snpEff [05:58:56] Found samclip - /usr/local/bin/samclip [05:58:56] Found seqtk - /usr/local/bin/seqtk [05:58:56] Found parallel - /usr/local/bin/parallel [05:58:56] Found freebayes - /usr/local/bin/freebayes [05:58:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:58:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:58:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:58:56] Found vcfuniq - /usr/local/bin/vcfuniq [05:58:56] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:58:56] Found gzip - /bin/gzip [05:58:56] Found vt - /usr/local/bin/vt [05:58:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:58:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:58:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:58:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:58:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:58:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:58:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:58:57] Using reference: /cvmfs/data.galaxyproject.org/byhand/microbes/eschColi_APEC_O1/seq/eschColi_APEC_O1.fa [05:58:57] Treating reference as 'fasta' format. [05:58:57] Will use 1 CPU cores. [05:58:57] Using read file: /corral4/main/objects/9/5/0/dataset_950f8e91-ffa2-498f-b788-3bc522be3ba4.dat [05:58:57] Creating folder: Resistance_70_fasta [05:58:57] Changing working directory: Resistance_70_fasta [05:58:57] Creating reference folder: reference [05:58:57] Extracting FASTA and GFF from reference. [05:58:57] Wrote 3 sequences to ref.fa [05:58:57] Wrote 0 features to ref.gff [05:58:57] Shredding /corral4/main/objects/9/5/0/dataset_950f8e91-ffa2-498f-b788-3bc522be3ba4.dat into pseudo-reads [05:59:02] Wrote 396876 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [05:59:02] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time. [05:59:02] Using BAM RG (Read Group) ID: Resistance_70_fasta [05:59:02] Running: samtools faidx reference/ref.fa 2>> snps.log [05:59:02] Error running command, check Resistance_70_fasta/snps.log
4[05:58:31] This is snippy 4.6.0
Show full stderr[05:58:31] This is snippy 4.6.0 [05:58:31] Written by Torsten Seemann [05:58:31] Obtained from https://github.com/tseemann/snippy [05:58:31] Detected operating system: linux [05:58:31] Enabling bundled linux tools. [05:58:31] Found bwa - /usr/local/bin/bwa [05:58:31] Found bcftools - /usr/local/bin/bcftools [05:58:31] Found samtools - /usr/local/bin/samtools [05:58:31] Found java - /usr/local/bin/java [05:58:31] Found snpEff - /usr/local/bin/snpEff [05:58:31] Found samclip - /usr/local/bin/samclip [05:58:31] Found seqtk - /usr/local/bin/seqtk [05:58:31] Found parallel - /usr/local/bin/parallel [05:58:31] Found freebayes - /usr/local/bin/freebayes [05:58:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:58:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:58:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:58:31] Found vcfuniq - /usr/local/bin/vcfuniq [05:58:31] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:58:31] Found gzip - /bin/gzip [05:58:31] Found vt - /usr/local/bin/vt [05:58:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:58:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:58:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:58:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:58:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:58:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:58:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:58:32] Using reference: /cvmfs/data.galaxyproject.org/byhand/microbes/eschColi_APEC_O1/seq/eschColi_APEC_O1.fa [05:58:32] Treating reference as 'fasta' format. [05:58:32] Will use 1 CPU cores. [05:58:32] Using read file: /corral4/main/objects/4/7/b/dataset_47b089a5-7ccc-49f2-b505-f2adb97b524c.dat [05:58:32] Creating folder: Resistance_93_fasta [05:58:32] Changing working directory: Resistance_93_fasta [05:58:32] Creating reference folder: reference [05:58:32] Extracting FASTA and GFF from reference. [05:58:32] Wrote 3 sequences to ref.fa [05:58:32] Wrote 0 features to ref.gff [05:58:32] Shredding /corral4/main/objects/4/7/b/dataset_47b089a5-7ccc-49f2-b505-f2adb97b524c.dat into pseudo-reads [05:58:37] Wrote 422488 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [05:58:37] Freebayes will process 1 chunks of 5589314 bp, 1 chunks at a time. [05:58:37] Using BAM RG (Read Group) ID: Resistance_93_fasta [05:58:38] Running: samtools faidx reference/ref.fa 2>> snps.log [05:58:38] Running: bwa index reference/ref.fa 2>> snps.log [05:58:41] Error running command, check Resistance_93_fasta/snps.log
4[07:05:57] This is snippy 4.6.0
Show full stderr[07:05:57] This is snippy 4.6.0 [07:05:57] Written by Torsten Seemann [07:05:57] Obtained from https://github.com/tseemann/snippy [07:05:57] Detected operating system: linux [07:05:57] Enabling bundled linux tools. [07:05:57] Found bwa - /usr/local/bin/bwa [07:05:57] Found bcftools - /usr/local/bin/bcftools [07:05:57] Found samtools - /usr/local/bin/samtools [07:05:57] Found java - /usr/local/bin/java [07:05:57] Found snpEff - /usr/local/bin/snpEff [07:05:57] Found samclip - /usr/local/bin/samclip [07:05:57] Found seqtk - /usr/local/bin/seqtk [07:05:57] Found parallel - /usr/local/bin/parallel [07:05:57] Found freebayes - /usr/local/bin/freebayes [07:05:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:05:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:05:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:05:57] Found vcfuniq - /usr/local/bin/vcfuniq [07:05:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:05:57] Found gzip - /bin/gzip [07:05:57] Found vt - /usr/local/bin/vt [07:05:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:05:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:05:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:05:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:05:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:05:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:05:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:05:58] Using reference: /corral4/main/objects/b/c/7/dataset_bc72f994-0ee8-49f5-b32a-d0eb5858fef9.dat [07:05:58] Treating reference as 'fasta' format. [07:05:58] Will use 1 CPU cores. [07:05:58] Using read file: /corral4/main/objects/f/9/1/dataset_f91c1dae-8edf-47ef-85e8-e7216580cbc0.dat [07:05:58] Creating folder: BVBRC_genome_sequence___2025_10_25T135718_903_fasta [07:05:58] Changing working directory: BVBRC_genome_sequence___2025_10_25T135718_903_fasta [07:05:58] Creating reference folder: reference [07:05:58] Extracting FASTA and GFF from reference. [07:05:58] Wrote 1 sequences to ref.fa [07:05:58] Wrote 0 features to ref.gff [07:05:58] Shredding /corral4/main/objects/f/9/1/dataset_f91c1dae-8edf-47ef-85e8-e7216580cbc0.dat into pseudo-reads [07:06:00] Wrote 221700 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [07:06:00] Freebayes will process 1 chunks of 2868471 bp, 1 chunks at a time. [07:06:00] Using BAM RG (Read Group) ID: BVBRC_genome_sequence___2025_10_25T135718_903_fasta [07:06:00] Running: samtools faidx reference/ref.fa 2>> snps.log [07:06:00] Running: bwa index reference/ref.fa 2>> snps.log [07:06:01] Error running command, check BVBRC_genome_sequence___2025_10_25T135718_903_fasta/snps.log
4[06:48:03] This is snippy 4.6.0
Show full stderr[06:48:03] This is snippy 4.6.0 [06:48:03] Written by Torsten Seemann [06:48:03] Obtained from https://github.com/tseemann/snippy [06:48:03] Detected operating system: linux [06:48:03] Enabling bundled linux tools. [06:48:03] Found bwa - /usr/local/bin/bwa [06:48:03] Found bcftools - /usr/local/bin/bcftools [06:48:03] Found samtools - /usr/local/bin/samtools [06:48:03] Found java - /usr/local/bin/java [06:48:03] Found snpEff - /usr/local/bin/snpEff [06:48:03] Found samclip - /usr/local/bin/samclip [06:48:03] Found seqtk - /usr/local/bin/seqtk [06:48:03] Found parallel - /usr/local/bin/parallel [06:48:03] Found freebayes - /usr/local/bin/freebayes [06:48:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:48:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:48:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:48:03] Found vcfuniq - /usr/local/bin/vcfuniq [06:48:03] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:48:03] Found gzip - /bin/gzip [06:48:03] Found vt - /usr/local/bin/vt [06:48:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:48:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:48:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:48:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:48:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:48:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:48:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:48:04] Please supply a reference FASTA/GBK/EMBL file with --reference
4[07:12:32] This is snippy 4.6.0
Show full stderr[07:12:32] This is snippy 4.6.0 [07:12:32] Written by Torsten Seemann [07:12:32] Obtained from https://github.com/tseemann/snippy [07:12:32] Detected operating system: linux [07:12:32] Enabling bundled linux tools. [07:12:32] Found bwa - /usr/local/bin/bwa [07:12:32] Found bcftools - /usr/local/bin/bcftools [07:12:32] Found samtools - /usr/local/bin/samtools [07:12:32] Found java - /usr/local/bin/java [07:12:32] Found snpEff - /usr/local/bin/snpEff [07:12:32] Found samclip - /usr/local/bin/samclip [07:12:32] Found seqtk - /usr/local/bin/seqtk [07:12:32] Found parallel - /usr/local/bin/parallel [07:12:32] Found freebayes - /usr/local/bin/freebayes [07:12:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:12:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:12:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:12:32] Found vcfuniq - /usr/local/bin/vcfuniq [07:12:32] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:12:32] Found gzip - /bin/gzip [07:12:32] Found vt - /usr/local/bin/vt [07:12:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:12:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:12:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:12:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:12:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:12:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:12:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:12:33] Please supply a reference FASTA/GBK/EMBL file with --reference
4[06:57:22] This is snippy 4.6.0
Show full stderr[06:57:22] This is snippy 4.6.0 [06:57:22] Written by Torsten Seemann [06:57:22] Obtained from https://github.com/tseemann/snippy [06:57:22] Detected operating system: linux [06:57:22] Enabling bundled linux tools. [06:57:22] Found bwa - /usr/local/bin/bwa [06:57:22] Found bcftools - /usr/local/bin/bcftools [06:57:22] Found samtools - /usr/local/bin/samtools [06:57:22] Found java - /usr/local/bin/java [06:57:22] Found snpEff - /usr/local/bin/snpEff [06:57:22] Found samclip - /usr/local/bin/samclip [06:57:22] Found seqtk - /usr/local/bin/seqtk [06:57:22] Found parallel - /usr/local/bin/parallel [06:57:22] Found freebayes - /usr/local/bin/freebayes [06:57:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:57:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:57:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:57:22] Found vcfuniq - /usr/local/bin/vcfuniq [06:57:22] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:57:22] Found gzip - /bin/gzip [06:57:22] Found vt - /usr/local/bin/vt [06:57:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:57:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:57:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:57:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:57:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:57:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:57:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:57:23] Please supply a reference FASTA/GBK/EMBL file with --reference
4[07:01:10] This is snippy 4.6.0
Show full stderr[07:01:10] This is snippy 4.6.0 [07:01:10] Written by Torsten Seemann [07:01:10] Obtained from https://github.com/tseemann/snippy [07:01:10] Detected operating system: linux [07:01:10] Enabling bundled linux tools. [07:01:10] Found bwa - /usr/local/bin/bwa [07:01:10] Found bcftools - /usr/local/bin/bcftools [07:01:10] Found samtools - /usr/local/bin/samtools [07:01:10] Found java - /usr/local/bin/java [07:01:10] Found snpEff - /usr/local/bin/snpEff [07:01:10] Found samclip - /usr/local/bin/samclip [07:01:10] Found seqtk - /usr/local/bin/seqtk [07:01:10] Found parallel - /usr/local/bin/parallel [07:01:10] Found freebayes - /usr/local/bin/freebayes [07:01:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:01:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:01:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:01:10] Found vcfuniq - /usr/local/bin/vcfuniq [07:01:10] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:01:10] Found gzip - /bin/gzip [07:01:10] Found vt - /usr/local/bin/vt [07:01:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:01:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:01:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:01:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:01:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:01:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:01:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:01:11] Please supply a reference FASTA/GBK/EMBL file with --reference
4[07:01:24] This is snippy 4.6.0
Show full stderr[07:01:24] This is snippy 4.6.0 [07:01:24] Written by Torsten Seemann [07:01:24] Obtained from https://github.com/tseemann/snippy [07:01:24] Detected operating system: linux [07:01:24] Enabling bundled linux tools. [07:01:24] Found bwa - /usr/local/bin/bwa [07:01:24] Found bcftools - /usr/local/bin/bcftools [07:01:24] Found samtools - /usr/local/bin/samtools [07:01:24] Found java - /usr/local/bin/java [07:01:24] Found snpEff - /usr/local/bin/snpEff [07:01:24] Found samclip - /usr/local/bin/samclip [07:01:24] Found seqtk - /usr/local/bin/seqtk [07:01:24] Found parallel - /usr/local/bin/parallel [07:01:24] Found freebayes - /usr/local/bin/freebayes [07:01:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:01:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:01:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:01:24] Found vcfuniq - /usr/local/bin/vcfuniq [07:01:24] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:01:24] Found gzip - /bin/gzip [07:01:24] Found vt - /usr/local/bin/vt [07:01:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:01:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:01:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:01:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:01:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:01:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:01:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:01:24] Please supply a reference FASTA/GBK/EMBL file with --reference
4[07:00:55] This is snippy 4.6.0
Show full stderr[07:00:55] This is snippy 4.6.0 [07:00:55] Written by Torsten Seemann [07:00:55] Obtained from https://github.com/tseemann/snippy [07:00:55] Detected operating system: linux [07:00:55] Enabling bundled linux tools. [07:00:55] Found bwa - /usr/local/bin/bwa [07:00:55] Found bcftools - /usr/local/bin/bcftools [07:00:55] Found samtools - /usr/local/bin/samtools [07:00:55] Found java - /usr/local/bin/java [07:00:55] Found snpEff - /usr/local/bin/snpEff [07:00:55] Found samclip - /usr/local/bin/samclip [07:00:55] Found seqtk - /usr/local/bin/seqtk [07:00:55] Found parallel - /usr/local/bin/parallel [07:00:55] Found freebayes - /usr/local/bin/freebayes [07:00:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:00:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:00:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:00:55] Found vcfuniq - /usr/local/bin/vcfuniq [07:00:55] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:00:55] Found gzip - /bin/gzip [07:00:55] Found vt - /usr/local/bin/vt [07:00:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:00:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:00:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:00:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:00:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:00:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:00:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:00:56] Please supply a reference FASTA/GBK/EMBL file with --reference
4[07:13:30] This is snippy 4.6.0
Show full stderr[07:13:30] This is snippy 4.6.0 [07:13:30] Written by Torsten Seemann [07:13:30] Obtained from https://github.com/tseemann/snippy [07:13:30] Detected operating system: linux [07:13:30] Enabling bundled linux tools. [07:13:30] Found bwa - /usr/local/bin/bwa [07:13:30] Found bcftools - /usr/local/bin/bcftools [07:13:30] Found samtools - /usr/local/bin/samtools [07:13:30] Found java - /usr/local/bin/java [07:13:30] Found snpEff - /usr/local/bin/snpEff [07:13:30] Found samclip - /usr/local/bin/samclip [07:13:30] Found seqtk - /usr/local/bin/seqtk [07:13:30] Found parallel - /usr/local/bin/parallel [07:13:30] Found freebayes - /usr/local/bin/freebayes [07:13:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:13:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:13:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:13:30] Found vcfuniq - /usr/local/bin/vcfuniq [07:13:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:13:30] Found gzip - /bin/gzip [07:13:31] Found vt - /usr/local/bin/vt [07:13:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:13:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:13:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:13:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:13:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:13:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:13:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:13:31] Please supply a reference FASTA/GBK/EMBL file with --reference
4[07:10:13] This is snippy 4.6.0
Show full stderr[07:10:13] This is snippy 4.6.0 [07:10:13] Written by Torsten Seemann [07:10:13] Obtained from https://github.com/tseemann/snippy [07:10:13] Detected operating system: linux [07:10:13] Enabling bundled linux tools. [07:10:13] Found bwa - /usr/local/bin/bwa [07:10:13] Found bcftools - /usr/local/bin/bcftools [07:10:13] Found samtools - /usr/local/bin/samtools [07:10:13] Found java - /usr/local/bin/java [07:10:13] Found snpEff - /usr/local/bin/snpEff [07:10:13] Found samclip - /usr/local/bin/samclip [07:10:13] Found seqtk - /usr/local/bin/seqtk [07:10:13] Found parallel - /usr/local/bin/parallel [07:10:13] Found freebayes - /usr/local/bin/freebayes [07:10:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:10:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:10:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:10:13] Found vcfuniq - /usr/local/bin/vcfuniq [07:10:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:10:13] Found gzip - /bin/gzip [07:10:13] Found vt - /usr/local/bin/vt [07:10:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:10:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:10:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:10:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:10:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:10:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:10:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:10:14] Please supply a reference FASTA/GBK/EMBL file with --reference
4[07:10:42] This is snippy 4.6.0
Show full stderr[07:10:42] This is snippy 4.6.0 [07:10:42] Written by Torsten Seemann [07:10:42] Obtained from https://github.com/tseemann/snippy [07:10:42] Detected operating system: linux [07:10:42] Enabling bundled linux tools. [07:10:42] Found bwa - /usr/local/bin/bwa [07:10:42] Found bcftools - /usr/local/bin/bcftools [07:10:42] Found samtools - /usr/local/bin/samtools [07:10:42] Found java - /usr/local/bin/java [07:10:42] Found snpEff - /usr/local/bin/snpEff [07:10:42] Found samclip - /usr/local/bin/samclip [07:10:42] Found seqtk - /usr/local/bin/seqtk [07:10:42] Found parallel - /usr/local/bin/parallel [07:10:42] Found freebayes - /usr/local/bin/freebayes [07:10:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:10:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:10:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:10:42] Found vcfuniq - /usr/local/bin/vcfuniq [07:10:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:10:42] Found gzip - /bin/gzip [07:10:42] Found vt - /usr/local/bin/vt [07:10:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:10:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:10:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:10:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:10:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:10:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:10:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:10:43] Please supply a reference FASTA/GBK/EMBL file with --reference
4[07:14:41] This is snippy 4.6.0
Show full stderr[07:14:41] This is snippy 4.6.0 [07:14:41] Written by Torsten Seemann [07:14:41] Obtained from https://github.com/tseemann/snippy [07:14:41] Detected operating system: linux [07:14:41] Enabling bundled linux tools. [07:14:41] Found bwa - /usr/local/bin/bwa [07:14:41] Found bcftools - /usr/local/bin/bcftools [07:14:41] Found samtools - /usr/local/bin/samtools [07:14:41] Found java - /usr/local/bin/java [07:14:41] Found snpEff - /usr/local/bin/snpEff [07:14:41] Found samclip - /usr/local/bin/samclip [07:14:41] Found seqtk - /usr/local/bin/seqtk [07:14:41] Found parallel - /usr/local/bin/parallel [07:14:41] Found freebayes - /usr/local/bin/freebayes [07:14:41] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:14:41] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:14:41] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:14:41] Found vcfuniq - /usr/local/bin/vcfuniq [07:14:41] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:14:41] Found gzip - /bin/gzip [07:14:41] Found vt - /usr/local/bin/vt [07:14:41] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:14:41] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:14:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:14:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:14:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:14:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:14:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:14:41] Please supply a reference FASTA/GBK/EMBL file with --reference
4[07:14:14] This is snippy 4.6.0
Show full stderr[07:14:14] This is snippy 4.6.0 [07:14:14] Written by Torsten Seemann [07:14:14] Obtained from https://github.com/tseemann/snippy [07:14:14] Detected operating system: linux [07:14:14] Enabling bundled linux tools. [07:14:14] Found bwa - /usr/local/bin/bwa [07:14:14] Found bcftools - /usr/local/bin/bcftools [07:14:14] Found samtools - /usr/local/bin/samtools [07:14:14] Found java - /usr/local/bin/java [07:14:14] Found snpEff - /usr/local/bin/snpEff [07:14:14] Found samclip - /usr/local/bin/samclip [07:14:14] Found seqtk - /usr/local/bin/seqtk [07:14:14] Found parallel - /usr/local/bin/parallel [07:14:14] Found freebayes - /usr/local/bin/freebayes [07:14:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:14:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:14:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:14:14] Found vcfuniq - /usr/local/bin/vcfuniq [07:14:14] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:14:14] Found gzip - /bin/gzip [07:14:14] Found vt - /usr/local/bin/vt [07:14:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:14:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:14:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:14:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:14:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:14:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:14:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:14:15] Please supply a reference FASTA/GBK/EMBL file with --reference
4[07:25:35] This is snippy 4.6.0
Show full stderr[07:25:35] This is snippy 4.6.0 [07:25:35] Written by Torsten Seemann [07:25:35] Obtained from https://github.com/tseemann/snippy [07:25:35] Detected operating system: linux [07:25:35] Enabling bundled linux tools. [07:25:35] Found bwa - /usr/local/bin/bwa [07:25:35] Found bcftools - /usr/local/bin/bcftools [07:25:35] Found samtools - /usr/local/bin/samtools [07:25:35] Found java - /usr/local/bin/java [07:25:35] Found snpEff - /usr/local/bin/snpEff [07:25:35] Found samclip - /usr/local/bin/samclip [07:25:35] Found seqtk - /usr/local/bin/seqtk [07:25:35] Found parallel - /usr/local/bin/parallel [07:25:35] Found freebayes - /usr/local/bin/freebayes [07:25:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:25:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:25:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:25:35] Found vcfuniq - /usr/local/bin/vcfuniq [07:25:35] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:25:35] Found gzip - /bin/gzip [07:25:35] Found vt - /usr/local/bin/vt [07:25:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:25:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:25:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:25:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:25:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:25:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:25:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:25:36] Using reference: /corral4/main/objects/b/c/7/dataset_bc72f994-0ee8-49f5-b32a-d0eb5858fef9.dat [07:25:36] Treating reference as 'fasta' format. [07:25:36] Will use 1 CPU cores. [07:25:36] Using read file: /corral4/main/objects/0/e/9/dataset_0e967aab-1d11-4057-ab74-1b27a9a4c8ef.dat [07:25:36] Creating folder: BVBRC_genome_sequence__78__fasta [07:25:36] Changing working directory: BVBRC_genome_sequence__78__fasta [07:25:36] Creating reference folder: reference [07:25:36] Extracting FASTA and GFF from reference. [07:25:36] Wrote 1 sequences to ref.fa [07:25:36] Wrote 0 features to ref.gff [07:25:36] Shredding /corral4/main/objects/0/e/9/dataset_0e967aab-1d11-4057-ab74-1b27a9a4c8ef.dat into pseudo-reads [07:25:39] Wrote 216932 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [07:25:39] Freebayes will process 1 chunks of 2868471 bp, 1 chunks at a time. [07:25:39] Using BAM RG (Read Group) ID: BVBRC_genome_sequence__78__fasta [07:25:39] Running: samtools faidx reference/ref.fa 2>> snps.log [07:25:39] Running: bwa index reference/ref.fa 2>> snps.log [07:25:40] Error running command, check BVBRC_genome_sequence__78__fasta/snps.log
4[07:28:00] This is snippy 4.6.0
Show full stderr[07:28:00] This is snippy 4.6.0 [07:28:00] Written by Torsten Seemann [07:28:00] Obtained from https://github.com/tseemann/snippy [07:28:00] Detected operating system: linux [07:28:00] Enabling bundled linux tools. [07:28:00] Found bwa - /usr/local/bin/bwa [07:28:00] Found bcftools - /usr/local/bin/bcftools [07:28:00] Found samtools - /usr/local/bin/samtools [07:28:00] Found java - /usr/local/bin/java [07:28:01] Found snpEff - /usr/local/bin/snpEff [07:28:01] Found samclip - /usr/local/bin/samclip [07:28:01] Found seqtk - /usr/local/bin/seqtk [07:28:01] Found parallel - /usr/local/bin/parallel [07:28:01] Found freebayes - /usr/local/bin/freebayes [07:28:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:28:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:28:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:28:01] Found vcfuniq - /usr/local/bin/vcfuniq [07:28:01] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:28:01] Found gzip - /bin/gzip [07:28:01] Found vt - /usr/local/bin/vt [07:28:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:28:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:28:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:28:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:28:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:28:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:28:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:28:01] Please supply a reference FASTA/GBK/EMBL file with --reference
4[07:33:32] This is snippy 4.6.0
Show full stderr[07:33:32] This is snippy 4.6.0 [07:33:32] Written by Torsten Seemann [07:33:32] Obtained from https://github.com/tseemann/snippy [07:33:32] Detected operating system: linux [07:33:32] Enabling bundled linux tools. [07:33:32] Found bwa - /usr/local/bin/bwa [07:33:32] Found bcftools - /usr/local/bin/bcftools [07:33:32] Found samtools - /usr/local/bin/samtools [07:33:32] Found java - /usr/local/bin/java [07:33:32] Found snpEff - /usr/local/bin/snpEff [07:33:32] Found samclip - /usr/local/bin/samclip [07:33:32] Found seqtk - /usr/local/bin/seqtk [07:33:32] Found parallel - /usr/local/bin/parallel [07:33:32] Found freebayes - /usr/local/bin/freebayes [07:33:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:33:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:33:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:33:32] Found vcfuniq - /usr/local/bin/vcfuniq [07:33:32] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:33:32] Found gzip - /bin/gzip [07:33:32] Found vt - /usr/local/bin/vt [07:33:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:33:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:33:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:33:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:33:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:33:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:33:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:33:33] Please supply a reference FASTA/GBK/EMBL file with --reference
4[09:21:19] This is snippy 4.6.0
Show full stderr[09:21:19] This is snippy 4.6.0 [09:21:19] Written by Torsten Seemann [09:21:19] Obtained from https://github.com/tseemann/snippy [09:21:19] Detected operating system: linux [09:21:19] Enabling bundled linux tools. [09:21:19] Found bwa - /usr/local/bin/bwa [09:21:19] Found bcftools - /usr/local/bin/bcftools [09:21:19] Found samtools - /usr/local/bin/samtools [09:21:19] Found java - /usr/local/bin/java [09:21:19] Found snpEff - /usr/local/bin/snpEff [09:21:19] Found samclip - /usr/local/bin/samclip [09:21:19] Found seqtk - /usr/local/bin/seqtk [09:21:19] Found parallel - /usr/local/bin/parallel [09:21:19] Found freebayes - /usr/local/bin/freebayes [09:21:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [09:21:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [09:21:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [09:21:19] Found vcfuniq - /usr/local/bin/vcfuniq [09:21:19] Found vcffirstheader - /usr/local/bin/vcffirstheader [09:21:19] Found gzip - /bin/gzip [09:21:19] Found vt - /usr/local/bin/vt [09:21:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [09:21:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [09:21:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [09:21:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [09:21:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [09:21:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [09:21:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [09:21:19] Using reference: /cvmfs/data.galaxyproject.org/byhand/Araly1/seq/Araly1.fa [09:21:20] Treating reference as 'fasta' format. [09:21:20] Will use 1 CPU cores. [09:21:20] Using read file: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat [09:21:20] Using read file: /corral4/main/objects/4/f/2/dataset_4f223e0c-0f27-465c-8f45-1036c8ca8fdb.dat [09:21:20] Creating folder: GCF_000195955_2_ASM19595v2_genomic_fna [09:21:20] Changing working directory: GCF_000195955_2_ASM19595v2_genomic_fna [09:21:20] Creating reference folder: reference [09:21:20] Extracting FASTA and GFF from reference. [09:21:27] Wrote 702 sequences to ref.fa [09:21:27] Wrote 0 features to ref.gff [09:21:28] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time. [09:21:28] Using BAM RG (Read Group) ID: GCF_000195955_2_ASM19595v2_genomic_fna [09:21:28] Running: samtools faidx reference/ref.fa 2>> snps.log [09:21:28] Error running command, check GCF_000195955_2_ASM19595v2_genomic_fna/snps.log
4[12:48:03] This is snippy 4.6.0
Show full stderr[12:48:03] This is snippy 4.6.0 [12:48:03] Written by Torsten Seemann [12:48:03] Obtained from https://github.com/tseemann/snippy [12:48:03] Detected operating system: linux [12:48:03] Enabling bundled linux tools. [12:48:03] Found bwa - /usr/local/bin/bwa [12:48:03] Found bcftools - /usr/local/bin/bcftools [12:48:03] Found samtools - /usr/local/bin/samtools [12:48:03] Found java - /usr/local/bin/java [12:48:03] Found snpEff - /usr/local/bin/snpEff [12:48:03] Found samclip - /usr/local/bin/samclip [12:48:03] Found seqtk - /usr/local/bin/seqtk [12:48:03] Found parallel - /usr/local/bin/parallel [12:48:03] Found freebayes - /usr/local/bin/freebayes [12:48:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:48:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:48:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:48:03] Found vcfuniq - /usr/local/bin/vcfuniq [12:48:03] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:48:03] Found gzip - /bin/gzip [12:48:03] Found vt - /usr/local/bin/vt [12:48:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:48:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:48:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:48:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:48:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:48:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:48:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:48:04] Please supply a reference FASTA/GBK/EMBL file with --reference
4[12:48:55] This is snippy 4.6.0
Show full stderr[12:48:55] This is snippy 4.6.0 [12:48:55] Written by Torsten Seemann [12:48:55] Obtained from https://github.com/tseemann/snippy [12:48:55] Detected operating system: linux [12:48:55] Enabling bundled linux tools. [12:48:55] Found bwa - /usr/local/bin/bwa [12:48:55] Found bcftools - /usr/local/bin/bcftools [12:48:55] Found samtools - /usr/local/bin/samtools [12:48:55] Found java - /usr/local/bin/java [12:48:55] Found snpEff - /usr/local/bin/snpEff [12:48:55] Found samclip - /usr/local/bin/samclip [12:48:55] Found seqtk - /usr/local/bin/seqtk [12:48:55] Found parallel - /usr/local/bin/parallel [12:48:55] Found freebayes - /usr/local/bin/freebayes [12:48:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:48:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:48:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:48:55] Found vcfuniq - /usr/local/bin/vcfuniq [12:48:55] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:48:55] Found gzip - /bin/gzip [12:48:55] Found vt - /usr/local/bin/vt [12:48:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:48:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:48:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:48:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:48:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:48:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:48:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:48:56] Please supply a reference FASTA/GBK/EMBL file with --reference
4[19:40:25] This is snippy 4.6.0
Show full stderr[19:40:25] This is snippy 4.6.0 [19:40:25] Written by Torsten Seemann [19:40:25] Obtained from https://github.com/tseemann/snippy [19:40:25] Detected operating system: linux [19:40:25] Enabling bundled linux tools. [19:40:25] Found bwa - /usr/local/bin/bwa [19:40:25] Found bcftools - /usr/local/bin/bcftools [19:40:25] Found samtools - /usr/local/bin/samtools [19:40:25] Found java - /usr/local/bin/java [19:40:25] Found snpEff - /usr/local/bin/snpEff [19:40:25] Found samclip - /usr/local/bin/samclip [19:40:25] Found seqtk - /usr/local/bin/seqtk [19:40:25] Found parallel - /usr/local/bin/parallel [19:40:25] Found freebayes - /usr/local/bin/freebayes [19:40:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [19:40:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [19:40:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [19:40:25] Found vcfuniq - /usr/local/bin/vcfuniq [19:40:25] Found vcffirstheader - /usr/local/bin/vcffirstheader [19:40:25] Found gzip - /bin/gzip [19:40:25] Found vt - /usr/local/bin/vt [19:40:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [19:40:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [19:40:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [19:40:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [19:40:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [19:40:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [19:40:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [19:40:25] Please supply a reference FASTA/GBK/EMBL file with --reference
4[14:45:02] This is snippy 4.6.0
Show full stderr[14:45:02] This is snippy 4.6.0 [14:45:02] Written by Torsten Seemann [14:45:02] Obtained from https://github.com/tseemann/snippy [14:45:02] Detected operating system: linux [14:45:02] Enabling bundled linux tools. [14:45:02] Found bwa - /usr/local/bin/bwa [14:45:02] Found bcftools - /usr/local/bin/bcftools [14:45:02] Found samtools - /usr/local/bin/samtools [14:45:02] Found java - /usr/local/bin/java [14:45:02] Found snpEff - /usr/local/bin/snpEff [14:45:02] Found samclip - /usr/local/bin/samclip [14:45:02] Found seqtk - /usr/local/bin/seqtk [14:45:02] Found parallel - /usr/local/bin/parallel [14:45:02] Found freebayes - /usr/local/bin/freebayes [14:45:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:45:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:45:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:45:02] Found vcfuniq - /usr/local/bin/vcfuniq [14:45:02] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:45:02] Found gzip - /bin/gzip [14:45:02] Found vt - /usr/local/bin/vt [14:45:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:45:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:45:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:45:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:45:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:45:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:45:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:45:03] Please supply a reference FASTA/GBK/EMBL file with --reference
4[14:47:12] This is snippy 4.6.0
Show full stderr[14:47:12] This is snippy 4.6.0 [14:47:12] Written by Torsten Seemann [14:47:12] Obtained from https://github.com/tseemann/snippy [14:47:12] Detected operating system: linux [14:47:12] Enabling bundled linux tools. [14:47:12] Found bwa - /usr/local/bin/bwa [14:47:12] Found bcftools - /usr/local/bin/bcftools [14:47:12] Found samtools - /usr/local/bin/samtools [14:47:12] Found java - /usr/local/bin/java [14:47:12] Found snpEff - /usr/local/bin/snpEff [14:47:12] Found samclip - /usr/local/bin/samclip [14:47:12] Found seqtk - /usr/local/bin/seqtk [14:47:12] Found parallel - /usr/local/bin/parallel [14:47:12] Found freebayes - /usr/local/bin/freebayes [14:47:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:47:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:47:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:47:12] Found vcfuniq - /usr/local/bin/vcfuniq [14:47:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:47:12] Found gzip - /bin/gzip [14:47:12] Found vt - /usr/local/bin/vt [14:47:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:47:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:47:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:47:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:47:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:47:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:47:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:47:13] Please supply a reference FASTA/GBK/EMBL file with --reference
4[14:47:26] This is snippy 4.6.0
Show full stderr[14:47:26] This is snippy 4.6.0 [14:47:26] Written by Torsten Seemann [14:47:26] Obtained from https://github.com/tseemann/snippy [14:47:26] Detected operating system: linux [14:47:26] Enabling bundled linux tools. [14:47:26] Found bwa - /usr/local/bin/bwa [14:47:26] Found bcftools - /usr/local/bin/bcftools [14:47:26] Found samtools - /usr/local/bin/samtools [14:47:26] Found java - /usr/local/bin/java [14:47:26] Found snpEff - /usr/local/bin/snpEff [14:47:26] Found samclip - /usr/local/bin/samclip [14:47:26] Found seqtk - /usr/local/bin/seqtk [14:47:26] Found parallel - /usr/local/bin/parallel [14:47:26] Found freebayes - /usr/local/bin/freebayes [14:47:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:47:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:47:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:47:26] Found vcfuniq - /usr/local/bin/vcfuniq [14:47:26] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:47:26] Found gzip - /bin/gzip [14:47:26] Found vt - /usr/local/bin/vt [14:47:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:47:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:47:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:47:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:47:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:47:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:47:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:47:27] Please supply a reference FASTA/GBK/EMBL file with --reference
4[17:38:33] This is snippy 4.6.0
Show full stderr[17:38:33] This is snippy 4.6.0 [17:38:33] Written by Torsten Seemann [17:38:33] Obtained from https://github.com/tseemann/snippy [17:38:33] Detected operating system: linux [17:38:33] Enabling bundled linux tools. [17:38:33] Found bwa - /usr/local/bin/bwa [17:38:33] Found bcftools - /usr/local/bin/bcftools [17:38:33] Found samtools - /usr/local/bin/samtools [17:38:33] Found java - /usr/local/bin/java [17:38:33] Found snpEff - /usr/local/bin/snpEff [17:38:33] Found samclip - /usr/local/bin/samclip [17:38:33] Found seqtk - /usr/local/bin/seqtk [17:38:33] Found parallel - /usr/local/bin/parallel [17:38:33] Found freebayes - /usr/local/bin/freebayes [17:38:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:38:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:38:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:38:33] Found vcfuniq - /usr/local/bin/vcfuniq [17:38:33] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:38:33] Found gzip - /bin/gzip [17:38:33] Found vt - /usr/local/bin/vt [17:38:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:38:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:38:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:38:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:38:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:38:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:38:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:38:33] Please supply a reference FASTA/GBK/EMBL file with --reference
3[21:34:13] This is snippy 4.6.0
Show full stderr[21:34:13] This is snippy 4.6.0 [21:34:13] Written by Torsten Seemann [21:34:13] Obtained from https://github.com/tseemann/snippy [21:34:13] Detected operating system: linux [21:34:13] Enabling bundled linux tools. [21:34:13] Found bwa - /usr/local/bin/bwa [21:34:13] Found bcftools - /usr/local/bin/bcftools [21:34:13] Found samtools - /usr/local/bin/samtools [21:34:13] Found java - /usr/local/bin/java [21:34:13] Found snpEff - /usr/local/bin/snpEff [21:34:13] Found samclip - /usr/local/bin/samclip [21:34:13] Found seqtk - /usr/local/bin/seqtk [21:34:13] Found parallel - /usr/local/bin/parallel [21:34:13] Found freebayes - /usr/local/bin/freebayes [21:34:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:34:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:34:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:34:13] Found vcfuniq - /usr/local/bin/vcfuniq [21:34:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:34:13] Found gzip - /bin/gzip [21:34:13] Found vt - /usr/local/bin/vt [21:34:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:34:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:34:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:34:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:34:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:34:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:34:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:34:15] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat [21:34:15] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat'
3[21:34:28] This is snippy 4.6.0
Show full stderr[21:34:28] This is snippy 4.6.0 [21:34:28] Written by Torsten Seemann [21:34:28] Obtained from https://github.com/tseemann/snippy [21:34:28] Detected operating system: linux [21:34:28] Enabling bundled linux tools. [21:34:28] Found bwa - /usr/local/bin/bwa [21:34:28] Found bcftools - /usr/local/bin/bcftools [21:34:28] Found samtools - /usr/local/bin/samtools [21:34:28] Found java - /usr/local/bin/java [21:34:28] Found snpEff - /usr/local/bin/snpEff [21:34:28] Found samclip - /usr/local/bin/samclip [21:34:28] Found seqtk - /usr/local/bin/seqtk [21:34:28] Found parallel - /usr/local/bin/parallel [21:34:28] Found freebayes - /usr/local/bin/freebayes [21:34:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:34:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:34:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:34:28] Found vcfuniq - /usr/local/bin/vcfuniq [21:34:28] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:34:28] Found gzip - /bin/gzip [21:34:28] Found vt - /usr/local/bin/vt [21:34:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:34:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:34:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:34:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:34:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:34:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:34:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:34:29] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat [21:34:29] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat'
3[21:34:49] This is snippy 4.6.0
Show full stderr[21:34:49] This is snippy 4.6.0 [21:34:49] Written by Torsten Seemann [21:34:49] Obtained from https://github.com/tseemann/snippy [21:34:49] Detected operating system: linux [21:34:49] Enabling bundled linux tools. [21:34:49] Found bwa - /usr/local/bin/bwa [21:34:49] Found bcftools - /usr/local/bin/bcftools [21:34:49] Found samtools - /usr/local/bin/samtools [21:34:49] Found java - /usr/local/bin/java [21:34:49] Found snpEff - /usr/local/bin/snpEff [21:34:49] Found samclip - /usr/local/bin/samclip [21:34:49] Found seqtk - /usr/local/bin/seqtk [21:34:49] Found parallel - /usr/local/bin/parallel [21:34:49] Found freebayes - /usr/local/bin/freebayes [21:34:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:34:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:34:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:34:49] Found vcfuniq - /usr/local/bin/vcfuniq [21:34:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:34:49] Found gzip - /bin/gzip [21:34:49] Found vt - /usr/local/bin/vt [21:34:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:34:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:34:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:34:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:34:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:34:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:34:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:34:50] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat [21:34:50] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat'
3[04:37:53] This is snippy 4.6.0
Show full stderr[04:37:53] This is snippy 4.6.0 [04:37:53] Written by Torsten Seemann [04:37:53] Obtained from https://github.com/tseemann/snippy [04:37:53] Detected operating system: linux [04:37:53] Enabling bundled linux tools. [04:37:53] Found bwa - /usr/local/bin/bwa [04:37:53] Found bcftools - /usr/local/bin/bcftools [04:37:53] Found samtools - /usr/local/bin/samtools [04:37:53] Found java - /usr/local/bin/java [04:37:53] Found snpEff - /usr/local/bin/snpEff [04:37:53] Found samclip - /usr/local/bin/samclip [04:37:53] Found seqtk - /usr/local/bin/seqtk [04:37:53] Found parallel - /usr/local/bin/parallel [04:37:53] Found freebayes - /usr/local/bin/freebayes [04:37:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:37:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:37:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:37:53] Found vcfuniq - /usr/local/bin/vcfuniq [04:37:53] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:37:53] Found gzip - /bin/gzip [04:37:53] Found vt - /usr/local/bin/vt [04:37:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:37:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:37:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:37:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:37:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:37:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:37:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:37:54] Please supply a reference FASTA/GBK/EMBL file with --reference
3[04:39:21] This is snippy 4.6.0
Show full stderr[04:39:21] This is snippy 4.6.0 [04:39:21] Written by Torsten Seemann [04:39:21] Obtained from https://github.com/tseemann/snippy [04:39:21] Detected operating system: linux [04:39:21] Enabling bundled linux tools. [04:39:21] Found bwa - /usr/local/bin/bwa [04:39:21] Found bcftools - /usr/local/bin/bcftools [04:39:21] Found samtools - /usr/local/bin/samtools [04:39:21] Found java - /usr/local/bin/java [04:39:21] Found snpEff - /usr/local/bin/snpEff [04:39:21] Found samclip - /usr/local/bin/samclip [04:39:21] Found seqtk - /usr/local/bin/seqtk [04:39:21] Found parallel - /usr/local/bin/parallel [04:39:21] Found freebayes - /usr/local/bin/freebayes [04:39:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:39:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:39:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:39:21] Found vcfuniq - /usr/local/bin/vcfuniq [04:39:21] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:39:21] Found gzip - /bin/gzip [04:39:21] Found vt - /usr/local/bin/vt [04:39:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:39:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:39:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:39:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:39:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:39:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:39:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:39:22] Please supply a reference FASTA/GBK/EMBL file with --reference
3[04:37:27] This is snippy 4.6.0
Show full stderr[04:37:27] This is snippy 4.6.0 [04:37:27] Written by Torsten Seemann [04:37:27] Obtained from https://github.com/tseemann/snippy [04:37:27] Detected operating system: linux [04:37:27] Enabling bundled linux tools. [04:37:27] Found bwa - /usr/local/bin/bwa [04:37:27] Found bcftools - /usr/local/bin/bcftools [04:37:27] Found samtools - /usr/local/bin/samtools [04:37:27] Found java - /usr/local/bin/java [04:37:27] Found snpEff - /usr/local/bin/snpEff [04:37:27] Found samclip - /usr/local/bin/samclip [04:37:27] Found seqtk - /usr/local/bin/seqtk [04:37:27] Found parallel - /usr/local/bin/parallel [04:37:27] Found freebayes - /usr/local/bin/freebayes [04:37:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:37:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:37:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:37:27] Found vcfuniq - /usr/local/bin/vcfuniq [04:37:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:37:27] Found gzip - /bin/gzip [04:37:27] Found vt - /usr/local/bin/vt [04:37:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:37:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:37:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:37:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:37:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:37:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:37:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:37:28] Please supply a reference FASTA/GBK/EMBL file with --reference
3[04:37:59] This is snippy 4.6.0
Show full stderr[04:37:59] This is snippy 4.6.0 [04:37:59] Written by Torsten Seemann [04:37:59] Obtained from https://github.com/tseemann/snippy [04:37:59] Detected operating system: linux [04:37:59] Enabling bundled linux tools. [04:37:59] Found bwa - /usr/local/bin/bwa [04:37:59] Found bcftools - /usr/local/bin/bcftools [04:37:59] Found samtools - /usr/local/bin/samtools [04:37:59] Found java - /usr/local/bin/java [04:37:59] Found snpEff - /usr/local/bin/snpEff [04:37:59] Found samclip - /usr/local/bin/samclip [04:37:59] Found seqtk - /usr/local/bin/seqtk [04:37:59] Found parallel - /usr/local/bin/parallel [04:37:59] Found freebayes - /usr/local/bin/freebayes [04:37:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:37:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:37:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:37:59] Found vcfuniq - /usr/local/bin/vcfuniq [04:37:59] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:37:59] Found gzip - /bin/gzip [04:37:59] Found vt - /usr/local/bin/vt [04:37:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:37:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:37:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:37:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:37:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:37:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:37:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:37:59] Please supply a reference FASTA/GBK/EMBL file with --reference
3[04:39:57] This is snippy 4.6.0
Show full stderr[04:39:57] This is snippy 4.6.0 [04:39:57] Written by Torsten Seemann [04:39:57] Obtained from https://github.com/tseemann/snippy [04:39:57] Detected operating system: linux [04:39:57] Enabling bundled linux tools. [04:39:57] Found bwa - /usr/local/bin/bwa [04:39:57] Found bcftools - /usr/local/bin/bcftools [04:39:57] Found samtools - /usr/local/bin/samtools [04:39:57] Found java - /usr/local/bin/java [04:39:57] Found snpEff - /usr/local/bin/snpEff [04:39:57] Found samclip - /usr/local/bin/samclip [04:39:57] Found seqtk - /usr/local/bin/seqtk [04:39:57] Found parallel - /usr/local/bin/parallel [04:39:57] Found freebayes - /usr/local/bin/freebayes [04:39:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:39:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:39:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:39:57] Found vcfuniq - /usr/local/bin/vcfuniq [04:39:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:39:57] Found gzip - /bin/gzip [04:39:57] Found vt - /usr/local/bin/vt [04:39:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:39:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:39:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:39:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:39:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:39:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:39:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:39:58] Please supply a reference FASTA/GBK/EMBL file with --reference
3[04:37:15] This is snippy 4.6.0
Show full stderr[04:37:15] This is snippy 4.6.0 [04:37:15] Written by Torsten Seemann [04:37:15] Obtained from https://github.com/tseemann/snippy [04:37:15] Detected operating system: linux [04:37:15] Enabling bundled linux tools. [04:37:15] Found bwa - /usr/local/bin/bwa [04:37:15] Found bcftools - /usr/local/bin/bcftools [04:37:15] Found samtools - /usr/local/bin/samtools [04:37:15] Found java - /usr/local/bin/java [04:37:15] Found snpEff - /usr/local/bin/snpEff [04:37:15] Found samclip - /usr/local/bin/samclip [04:37:15] Found seqtk - /usr/local/bin/seqtk [04:37:15] Found parallel - /usr/local/bin/parallel [04:37:15] Found freebayes - /usr/local/bin/freebayes [04:37:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:37:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:37:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:37:15] Found vcfuniq - /usr/local/bin/vcfuniq [04:37:15] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:37:15] Found gzip - /bin/gzip [04:37:15] Found vt - /usr/local/bin/vt [04:37:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:37:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:37:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:37:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:37:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:37:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:37:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:37:15] Please supply a reference FASTA/GBK/EMBL file with --reference
3[04:39:39] This is snippy 4.6.0
Show full stderr[04:39:39] This is snippy 4.6.0 [04:39:39] Written by Torsten Seemann [04:39:39] Obtained from https://github.com/tseemann/snippy [04:39:39] Detected operating system: linux [04:39:39] Enabling bundled linux tools. [04:39:39] Found bwa - /usr/local/bin/bwa [04:39:39] Found bcftools - /usr/local/bin/bcftools [04:39:39] Found samtools - /usr/local/bin/samtools [04:39:39] Found java - /usr/local/bin/java [04:39:39] Found snpEff - /usr/local/bin/snpEff [04:39:39] Found samclip - /usr/local/bin/samclip [04:39:39] Found seqtk - /usr/local/bin/seqtk [04:39:39] Found parallel - /usr/local/bin/parallel [04:39:39] Found freebayes - /usr/local/bin/freebayes [04:39:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:39:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:39:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:39:39] Found vcfuniq - /usr/local/bin/vcfuniq [04:39:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:39:39] Found gzip - /bin/gzip [04:39:39] Found vt - /usr/local/bin/vt [04:39:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:39:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:39:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:39:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:39:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:39:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:39:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:39:40] Please supply a reference FASTA/GBK/EMBL file with --reference
3[04:40:29] This is snippy 4.6.0
Show full stderr[04:40:29] This is snippy 4.6.0 [04:40:29] Written by Torsten Seemann [04:40:29] Obtained from https://github.com/tseemann/snippy [04:40:29] Detected operating system: linux [04:40:29] Enabling bundled linux tools. [04:40:29] Found bwa - /usr/local/bin/bwa [04:40:29] Found bcftools - /usr/local/bin/bcftools [04:40:29] Found samtools - /usr/local/bin/samtools [04:40:29] Found java - /usr/local/bin/java [04:40:29] Found snpEff - /usr/local/bin/snpEff [04:40:29] Found samclip - /usr/local/bin/samclip [04:40:29] Found seqtk - /usr/local/bin/seqtk [04:40:29] Found parallel - /usr/local/bin/parallel [04:40:29] Found freebayes - /usr/local/bin/freebayes [04:40:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:40:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:40:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:40:29] Found vcfuniq - /usr/local/bin/vcfuniq [04:40:29] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:40:29] Found gzip - /bin/gzip [04:40:29] Found vt - /usr/local/bin/vt [04:40:29] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:40:29] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:40:29] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:40:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:40:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:40:30] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:40:30] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:40:30] Please supply a reference FASTA/GBK/EMBL file with --reference
3[04:39:24] This is snippy 4.6.0
Show full stderr[04:39:24] This is snippy 4.6.0 [04:39:24] Written by Torsten Seemann [04:39:24] Obtained from https://github.com/tseemann/snippy [04:39:24] Detected operating system: linux [04:39:24] Enabling bundled linux tools. [04:39:24] Found bwa - /usr/local/bin/bwa [04:39:24] Found bcftools - /usr/local/bin/bcftools [04:39:24] Found samtools - /usr/local/bin/samtools [04:39:24] Found java - /usr/local/bin/java [04:39:24] Found snpEff - /usr/local/bin/snpEff [04:39:24] Found samclip - /usr/local/bin/samclip [04:39:24] Found seqtk - /usr/local/bin/seqtk [04:39:24] Found parallel - /usr/local/bin/parallel [04:39:24] Found freebayes - /usr/local/bin/freebayes [04:39:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:39:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:39:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:39:24] Found vcfuniq - /usr/local/bin/vcfuniq [04:39:24] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:39:24] Found gzip - /bin/gzip [04:39:24] Found vt - /usr/local/bin/vt [04:39:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:39:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:39:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:39:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:39:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:39:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:39:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:39:25] Please supply a reference FASTA/GBK/EMBL file with --reference
3[04:40:44] This is snippy 4.6.0
Show full stderr[04:40:44] This is snippy 4.6.0 [04:40:44] Written by Torsten Seemann [04:40:44] Obtained from https://github.com/tseemann/snippy [04:40:44] Detected operating system: linux [04:40:44] Enabling bundled linux tools. [04:40:44] Found bwa - /usr/local/bin/bwa [04:40:44] Found bcftools - /usr/local/bin/bcftools [04:40:44] Found samtools - /usr/local/bin/samtools [04:40:44] Found java - /usr/local/bin/java [04:40:44] Found snpEff - /usr/local/bin/snpEff [04:40:44] Found samclip - /usr/local/bin/samclip [04:40:44] Found seqtk - /usr/local/bin/seqtk [04:40:44] Found parallel - /usr/local/bin/parallel [04:40:44] Found freebayes - /usr/local/bin/freebayes [04:40:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:40:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:40:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:40:44] Found vcfuniq - /usr/local/bin/vcfuniq [04:40:44] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:40:44] Found gzip - /bin/gzip [04:40:44] Found vt - /usr/local/bin/vt [04:40:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:40:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:40:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:40:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:40:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:40:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:40:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:40:45] Please supply a reference FASTA/GBK/EMBL file with --reference
3[04:40:56] This is snippy 4.6.0
Show full stderr[04:40:56] This is snippy 4.6.0 [04:40:56] Written by Torsten Seemann [04:40:56] Obtained from https://github.com/tseemann/snippy [04:40:56] Detected operating system: linux [04:40:56] Enabling bundled linux tools. [04:40:56] Found bwa - /usr/local/bin/bwa [04:40:56] Found bcftools - /usr/local/bin/bcftools [04:40:56] Found samtools - /usr/local/bin/samtools [04:40:56] Found java - /usr/local/bin/java [04:40:56] Found snpEff - /usr/local/bin/snpEff [04:40:56] Found samclip - /usr/local/bin/samclip [04:40:56] Found seqtk - /usr/local/bin/seqtk [04:40:56] Found parallel - /usr/local/bin/parallel [04:40:56] Found freebayes - /usr/local/bin/freebayes [04:40:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:40:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:40:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:40:56] Found vcfuniq - /usr/local/bin/vcfuniq [04:40:56] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:40:56] Found gzip - /bin/gzip [04:40:56] Found vt - /usr/local/bin/vt [04:40:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:40:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:40:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:40:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:40:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:40:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:40:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:40:57] Please supply a reference FASTA/GBK/EMBL file with --reference
3[04:41:09] This is snippy 4.6.0
Show full stderr[04:41:09] This is snippy 4.6.0 [04:41:09] Written by Torsten Seemann [04:41:09] Obtained from https://github.com/tseemann/snippy [04:41:09] Detected operating system: linux [04:41:09] Enabling bundled linux tools. [04:41:09] Found bwa - /usr/local/bin/bwa [04:41:09] Found bcftools - /usr/local/bin/bcftools [04:41:09] Found samtools - /usr/local/bin/samtools [04:41:09] Found java - /usr/local/bin/java [04:41:09] Found snpEff - /usr/local/bin/snpEff [04:41:09] Found samclip - /usr/local/bin/samclip [04:41:09] Found seqtk - /usr/local/bin/seqtk [04:41:09] Found parallel - /usr/local/bin/parallel [04:41:09] Found freebayes - /usr/local/bin/freebayes [04:41:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:41:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:41:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:41:09] Found vcfuniq - /usr/local/bin/vcfuniq [04:41:09] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:41:09] Found gzip - /bin/gzip [04:41:09] Found vt - /usr/local/bin/vt [04:41:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:41:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:41:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:41:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:41:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:41:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:41:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:41:10] Please supply a reference FASTA/GBK/EMBL file with --reference
3[04:41:24] This is snippy 4.6.0
Show full stderr[04:41:24] This is snippy 4.6.0 [04:41:24] Written by Torsten Seemann [04:41:24] Obtained from https://github.com/tseemann/snippy [04:41:24] Detected operating system: linux [04:41:24] Enabling bundled linux tools. [04:41:24] Found bwa - /usr/local/bin/bwa [04:41:24] Found bcftools - /usr/local/bin/bcftools [04:41:24] Found samtools - /usr/local/bin/samtools [04:41:24] Found java - /usr/local/bin/java [04:41:24] Found snpEff - /usr/local/bin/snpEff [04:41:24] Found samclip - /usr/local/bin/samclip [04:41:24] Found seqtk - /usr/local/bin/seqtk [04:41:24] Found parallel - /usr/local/bin/parallel [04:41:24] Found freebayes - /usr/local/bin/freebayes [04:41:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:41:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:41:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:41:24] Found vcfuniq - /usr/local/bin/vcfuniq [04:41:24] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:41:24] Found gzip - /bin/gzip [04:41:24] Found vt - /usr/local/bin/vt [04:41:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:41:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:41:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:41:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:41:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:41:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:41:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:41:25] Please supply a reference FASTA/GBK/EMBL file with --reference
3[04:42:21] This is snippy 4.6.0
Show full stderr[04:42:21] This is snippy 4.6.0 [04:42:21] Written by Torsten Seemann [04:42:21] Obtained from https://github.com/tseemann/snippy [04:42:21] Detected operating system: linux [04:42:21] Enabling bundled linux tools. [04:42:21] Found bwa - /usr/local/bin/bwa [04:42:21] Found bcftools - /usr/local/bin/bcftools [04:42:21] Found samtools - /usr/local/bin/samtools [04:42:21] Found java - /usr/local/bin/java [04:42:21] Found snpEff - /usr/local/bin/snpEff [04:42:21] Found samclip - /usr/local/bin/samclip [04:42:21] Found seqtk - /usr/local/bin/seqtk [04:42:21] Found parallel - /usr/local/bin/parallel [04:42:21] Found freebayes - /usr/local/bin/freebayes [04:42:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:42:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:42:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:42:21] Found vcfuniq - /usr/local/bin/vcfuniq [04:42:21] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:42:21] Found gzip - /bin/gzip [04:42:21] Found vt - /usr/local/bin/vt [04:42:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:42:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:42:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:42:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:42:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:42:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:42:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:42:23] Please supply a reference FASTA/GBK/EMBL file with --reference
3[04:41:46] This is snippy 4.6.0
Show full stderr[04:41:46] This is snippy 4.6.0 [04:41:46] Written by Torsten Seemann [04:41:46] Obtained from https://github.com/tseemann/snippy [04:41:46] Detected operating system: linux [04:41:46] Enabling bundled linux tools. [04:41:46] Found bwa - /usr/local/bin/bwa [04:41:46] Found bcftools - /usr/local/bin/bcftools [04:41:46] Found samtools - /usr/local/bin/samtools [04:41:46] Found java - /usr/local/bin/java [04:41:46] Found snpEff - /usr/local/bin/snpEff [04:41:46] Found samclip - /usr/local/bin/samclip [04:41:46] Found seqtk - /usr/local/bin/seqtk [04:41:46] Found parallel - /usr/local/bin/parallel [04:41:46] Found freebayes - /usr/local/bin/freebayes [04:41:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:41:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:41:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:41:46] Found vcfuniq - /usr/local/bin/vcfuniq [04:41:46] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:41:46] Found gzip - /bin/gzip [04:41:46] Found vt - /usr/local/bin/vt [04:41:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:41:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:41:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:41:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:41:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:41:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:41:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:41:47] Please supply a reference FASTA/GBK/EMBL file with --reference
3[04:43:03] This is snippy 4.6.0
Show full stderr[04:43:03] This is snippy 4.6.0 [04:43:03] Written by Torsten Seemann [04:43:03] Obtained from https://github.com/tseemann/snippy [04:43:03] Detected operating system: linux [04:43:03] Enabling bundled linux tools. [04:43:03] Found bwa - /usr/local/bin/bwa [04:43:03] Found bcftools - /usr/local/bin/bcftools [04:43:03] Found samtools - /usr/local/bin/samtools [04:43:03] Found java - /usr/local/bin/java [04:43:03] Found snpEff - /usr/local/bin/snpEff [04:43:03] Found samclip - /usr/local/bin/samclip [04:43:03] Found seqtk - /usr/local/bin/seqtk [04:43:03] Found parallel - /usr/local/bin/parallel [04:43:03] Found freebayes - /usr/local/bin/freebayes [04:43:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:43:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:43:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:43:03] Found vcfuniq - /usr/local/bin/vcfuniq [04:43:03] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:43:03] Found gzip - /bin/gzip [04:43:03] Found vt - /usr/local/bin/vt [04:43:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:43:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:43:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:43:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:43:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:43:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:43:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:43:05] Please supply a reference FASTA/GBK/EMBL file with --reference
3[04:44:46] This is snippy 4.6.0
Show full stderr[04:44:46] This is snippy 4.6.0 [04:44:46] Written by Torsten Seemann [04:44:46] Obtained from https://github.com/tseemann/snippy [04:44:46] Detected operating system: linux [04:44:46] Enabling bundled linux tools. [04:44:46] Found bwa - /usr/local/bin/bwa [04:44:46] Found bcftools - /usr/local/bin/bcftools [04:44:46] Found samtools - /usr/local/bin/samtools [04:44:46] Found java - /usr/local/bin/java [04:44:46] Found snpEff - /usr/local/bin/snpEff [04:44:46] Found samclip - /usr/local/bin/samclip [04:44:46] Found seqtk - /usr/local/bin/seqtk [04:44:46] Found parallel - /usr/local/bin/parallel [04:44:46] Found freebayes - /usr/local/bin/freebayes [04:44:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:44:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:44:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:44:46] Found vcfuniq - /usr/local/bin/vcfuniq [04:44:46] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:44:46] Found gzip - /bin/gzip [04:44:46] Found vt - /usr/local/bin/vt [04:44:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:44:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:44:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:44:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:44:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:44:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:44:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:44:47] Please supply a reference FASTA/GBK/EMBL file with --reference
3[04:43:24] This is snippy 4.6.0
Show full stderr[04:43:24] This is snippy 4.6.0 [04:43:24] Written by Torsten Seemann [04:43:24] Obtained from https://github.com/tseemann/snippy [04:43:24] Detected operating system: linux [04:43:24] Enabling bundled linux tools. [04:43:24] Found bwa - /usr/local/bin/bwa [04:43:24] Found bcftools - /usr/local/bin/bcftools [04:43:24] Found samtools - /usr/local/bin/samtools [04:43:24] Found java - /usr/local/bin/java [04:43:24] Found snpEff - /usr/local/bin/snpEff [04:43:24] Found samclip - /usr/local/bin/samclip [04:43:24] Found seqtk - /usr/local/bin/seqtk [04:43:24] Found parallel - /usr/local/bin/parallel [04:43:24] Found freebayes - /usr/local/bin/freebayes [04:43:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:43:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:43:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:43:24] Found vcfuniq - /usr/local/bin/vcfuniq [04:43:24] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:43:24] Found gzip - /bin/gzip [04:43:24] Found vt - /usr/local/bin/vt [04:43:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:43:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:43:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:43:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:43:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:43:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:43:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:43:25] Please supply a reference FASTA/GBK/EMBL file with --reference
3[04:43:21] This is snippy 4.6.0
Show full stderr[04:43:21] This is snippy 4.6.0 [04:43:21] Written by Torsten Seemann [04:43:21] Obtained from https://github.com/tseemann/snippy [04:43:21] Detected operating system: linux [04:43:21] Enabling bundled linux tools. [04:43:21] Found bwa - /usr/local/bin/bwa [04:43:21] Found bcftools - /usr/local/bin/bcftools [04:43:21] Found samtools - /usr/local/bin/samtools [04:43:21] Found java - /usr/local/bin/java [04:43:21] Found snpEff - /usr/local/bin/snpEff [04:43:21] Found samclip - /usr/local/bin/samclip [04:43:21] Found seqtk - /usr/local/bin/seqtk [04:43:21] Found parallel - /usr/local/bin/parallel [04:43:21] Found freebayes - /usr/local/bin/freebayes [04:43:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:43:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:43:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:43:21] Found vcfuniq - /usr/local/bin/vcfuniq [04:43:21] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:43:21] Found gzip - /bin/gzip [04:43:21] Found vt - /usr/local/bin/vt [04:43:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:43:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:43:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:43:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:43:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:43:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:43:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:43:22] Please supply a reference FASTA/GBK/EMBL file with --reference
3[04:55:03] This is snippy 4.6.0
Show full stderr[04:55:03] This is snippy 4.6.0 [04:55:03] Written by Torsten Seemann [04:55:03] Obtained from https://github.com/tseemann/snippy [04:55:03] Detected operating system: linux [04:55:03] Enabling bundled linux tools. [04:55:03] Found bwa - /usr/local/bin/bwa [04:55:03] Found bcftools - /usr/local/bin/bcftools [04:55:03] Found samtools - /usr/local/bin/samtools [04:55:03] Found java - /usr/local/bin/java [04:55:03] Found snpEff - /usr/local/bin/snpEff [04:55:03] Found samclip - /usr/local/bin/samclip [04:55:03] Found seqtk - /usr/local/bin/seqtk [04:55:03] Found parallel - /usr/local/bin/parallel [04:55:03] Found freebayes - /usr/local/bin/freebayes [04:55:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:55:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:55:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:55:03] Found vcfuniq - /usr/local/bin/vcfuniq [04:55:03] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:55:03] Found gzip - /bin/gzip [04:55:03] Found vt - /usr/local/bin/vt [04:55:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:55:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:55:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:55:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:55:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:55:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:55:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:55:04] Please supply a reference FASTA/GBK/EMBL file with --reference
3[04:55:46] This is snippy 4.6.0
Show full stderr[04:55:46] This is snippy 4.6.0 [04:55:46] Written by Torsten Seemann [04:55:46] Obtained from https://github.com/tseemann/snippy [04:55:46] Detected operating system: linux [04:55:46] Enabling bundled linux tools. [04:55:46] Found bwa - /usr/local/bin/bwa [04:55:46] Found bcftools - /usr/local/bin/bcftools [04:55:46] Found samtools - /usr/local/bin/samtools [04:55:46] Found java - /usr/local/bin/java [04:55:46] Found snpEff - /usr/local/bin/snpEff [04:55:46] Found samclip - /usr/local/bin/samclip [04:55:46] Found seqtk - /usr/local/bin/seqtk [04:55:46] Found parallel - /usr/local/bin/parallel [04:55:46] Found freebayes - /usr/local/bin/freebayes [04:55:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:55:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:55:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:55:46] Found vcfuniq - /usr/local/bin/vcfuniq [04:55:46] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:55:46] Found gzip - /bin/gzip [04:55:46] Found vt - /usr/local/bin/vt [04:55:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:55:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:55:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:55:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:55:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:55:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:55:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:55:47] Please supply a reference FASTA/GBK/EMBL file with --reference
3[04:55:18] This is snippy 4.6.0
Show full stderr[04:55:18] This is snippy 4.6.0 [04:55:18] Written by Torsten Seemann [04:55:18] Obtained from https://github.com/tseemann/snippy [04:55:18] Detected operating system: linux [04:55:18] Enabling bundled linux tools. [04:55:18] Found bwa - /usr/local/bin/bwa [04:55:18] Found bcftools - /usr/local/bin/bcftools [04:55:18] Found samtools - /usr/local/bin/samtools [04:55:18] Found java - /usr/local/bin/java [04:55:18] Found snpEff - /usr/local/bin/snpEff [04:55:18] Found samclip - /usr/local/bin/samclip [04:55:18] Found seqtk - /usr/local/bin/seqtk [04:55:18] Found parallel - /usr/local/bin/parallel [04:55:18] Found freebayes - /usr/local/bin/freebayes [04:55:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:55:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:55:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:55:18] Found vcfuniq - /usr/local/bin/vcfuniq [04:55:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:55:18] Found gzip - /bin/gzip [04:55:18] Found vt - /usr/local/bin/vt [04:55:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:55:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:55:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:55:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:55:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:55:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:55:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:55:19] Please supply a reference FASTA/GBK/EMBL file with --reference
3[04:55:33] This is snippy 4.6.0
Show full stderr[04:55:33] This is snippy 4.6.0 [04:55:33] Written by Torsten Seemann [04:55:33] Obtained from https://github.com/tseemann/snippy [04:55:33] Detected operating system: linux [04:55:33] Enabling bundled linux tools. [04:55:33] Found bwa - /usr/local/bin/bwa [04:55:33] Found bcftools - /usr/local/bin/bcftools [04:55:33] Found samtools - /usr/local/bin/samtools [04:55:33] Found java - /usr/local/bin/java [04:55:33] Found snpEff - /usr/local/bin/snpEff [04:55:33] Found samclip - /usr/local/bin/samclip [04:55:33] Found seqtk - /usr/local/bin/seqtk [04:55:33] Found parallel - /usr/local/bin/parallel [04:55:33] Found freebayes - /usr/local/bin/freebayes [04:55:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:55:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:55:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:55:33] Found vcfuniq - /usr/local/bin/vcfuniq [04:55:33] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:55:33] Found gzip - /bin/gzip [04:55:33] Found vt - /usr/local/bin/vt [04:55:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:55:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:55:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:55:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:55:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:55:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:55:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:55:34] Please supply a reference FASTA/GBK/EMBL file with --reference
3[04:56:42] This is snippy 4.6.0
Show full stderr[04:56:42] This is snippy 4.6.0 [04:56:42] Written by Torsten Seemann [04:56:42] Obtained from https://github.com/tseemann/snippy [04:56:42] Detected operating system: linux [04:56:42] Enabling bundled linux tools. [04:56:42] Found bwa - /usr/local/bin/bwa [04:56:42] Found bcftools - /usr/local/bin/bcftools [04:56:42] Found samtools - /usr/local/bin/samtools [04:56:42] Found java - /usr/local/bin/java [04:56:42] Found snpEff - /usr/local/bin/snpEff [04:56:42] Found samclip - /usr/local/bin/samclip [04:56:42] Found seqtk - /usr/local/bin/seqtk [04:56:42] Found parallel - /usr/local/bin/parallel [04:56:42] Found freebayes - /usr/local/bin/freebayes [04:56:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:56:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:56:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:56:42] Found vcfuniq - /usr/local/bin/vcfuniq [04:56:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:56:42] Found gzip - /bin/gzip [04:56:42] Found vt - /usr/local/bin/vt [04:56:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:56:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:56:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:56:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:56:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:56:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:56:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:56:43] Please supply a reference FASTA/GBK/EMBL file with --reference
3[04:58:06] This is snippy 4.6.0
Show full stderr[04:58:06] This is snippy 4.6.0 [04:58:06] Written by Torsten Seemann [04:58:06] Obtained from https://github.com/tseemann/snippy [04:58:06] Detected operating system: linux [04:58:06] Enabling bundled linux tools. [04:58:06] Found bwa - /usr/local/bin/bwa [04:58:06] Found bcftools - /usr/local/bin/bcftools [04:58:06] Found samtools - /usr/local/bin/samtools [04:58:06] Found java - /usr/local/bin/java [04:58:06] Found snpEff - /usr/local/bin/snpEff [04:58:06] Found samclip - /usr/local/bin/samclip [04:58:06] Found seqtk - /usr/local/bin/seqtk [04:58:06] Found parallel - /usr/local/bin/parallel [04:58:06] Found freebayes - /usr/local/bin/freebayes [04:58:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:58:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:58:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:58:06] Found vcfuniq - /usr/local/bin/vcfuniq [04:58:06] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:58:06] Found gzip - /bin/gzip [04:58:06] Found vt - /usr/local/bin/vt [04:58:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:58:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:58:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:58:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:58:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:58:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:58:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:58:07] Please supply a reference FASTA/GBK/EMBL file with --reference
3[04:57:51] This is snippy 4.6.0
Show full stderr[04:57:51] This is snippy 4.6.0 [04:57:51] Written by Torsten Seemann [04:57:51] Obtained from https://github.com/tseemann/snippy [04:57:51] Detected operating system: linux [04:57:51] Enabling bundled linux tools. [04:57:51] Found bwa - /usr/local/bin/bwa [04:57:51] Found bcftools - /usr/local/bin/bcftools [04:57:51] Found samtools - /usr/local/bin/samtools [04:57:51] Found java - /usr/local/bin/java [04:57:51] Found snpEff - /usr/local/bin/snpEff [04:57:51] Found samclip - /usr/local/bin/samclip [04:57:51] Found seqtk - /usr/local/bin/seqtk [04:57:51] Found parallel - /usr/local/bin/parallel [04:57:51] Found freebayes - /usr/local/bin/freebayes [04:57:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:57:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:57:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:57:51] Found vcfuniq - /usr/local/bin/vcfuniq [04:57:51] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:57:51] Found gzip - /bin/gzip [04:57:51] Found vt - /usr/local/bin/vt [04:57:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:57:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:57:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:57:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:57:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:57:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:57:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:57:52] Please supply a reference FASTA/GBK/EMBL file with --reference
3[04:57:39] This is snippy 4.6.0
Show full stderr[04:57:39] This is snippy 4.6.0 [04:57:39] Written by Torsten Seemann [04:57:39] Obtained from https://github.com/tseemann/snippy [04:57:39] Detected operating system: linux [04:57:39] Enabling bundled linux tools. [04:57:39] Found bwa - /usr/local/bin/bwa [04:57:39] Found bcftools - /usr/local/bin/bcftools [04:57:39] Found samtools - /usr/local/bin/samtools [04:57:39] Found java - /usr/local/bin/java [04:57:39] Found snpEff - /usr/local/bin/snpEff [04:57:39] Found samclip - /usr/local/bin/samclip [04:57:39] Found seqtk - /usr/local/bin/seqtk [04:57:39] Found parallel - /usr/local/bin/parallel [04:57:39] Found freebayes - /usr/local/bin/freebayes [04:57:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:57:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:57:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:57:39] Found vcfuniq - /usr/local/bin/vcfuniq [04:57:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:57:39] Found gzip - /bin/gzip [04:57:39] Found vt - /usr/local/bin/vt [04:57:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:57:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:57:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:57:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:57:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:57:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:57:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:57:40] Please supply a reference FASTA/GBK/EMBL file with --reference
3[05:00:30] This is snippy 4.6.0
Show full stderr[05:00:30] This is snippy 4.6.0 [05:00:30] Written by Torsten Seemann [05:00:30] Obtained from https://github.com/tseemann/snippy [05:00:30] Detected operating system: linux [05:00:30] Enabling bundled linux tools. [05:00:30] Found bwa - /usr/local/bin/bwa [05:00:30] Found bcftools - /usr/local/bin/bcftools [05:00:30] Found samtools - /usr/local/bin/samtools [05:00:30] Found java - /usr/local/bin/java [05:00:30] Found snpEff - /usr/local/bin/snpEff [05:00:30] Found samclip - /usr/local/bin/samclip [05:00:30] Found seqtk - /usr/local/bin/seqtk [05:00:30] Found parallel - /usr/local/bin/parallel [05:00:30] Found freebayes - /usr/local/bin/freebayes [05:00:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:00:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:00:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:00:30] Found vcfuniq - /usr/local/bin/vcfuniq [05:00:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:00:30] Found gzip - /bin/gzip [05:00:30] Found vt - /usr/local/bin/vt [05:00:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:00:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:00:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:00:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:00:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:00:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:00:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:00:31] Please supply a reference FASTA/GBK/EMBL file with --reference
3[05:00:45] This is snippy 4.6.0
Show full stderr[05:00:45] This is snippy 4.6.0 [05:00:45] Written by Torsten Seemann [05:00:45] Obtained from https://github.com/tseemann/snippy [05:00:45] Detected operating system: linux [05:00:45] Enabling bundled linux tools. [05:00:45] Found bwa - /usr/local/bin/bwa [05:00:45] Found bcftools - /usr/local/bin/bcftools [05:00:45] Found samtools - /usr/local/bin/samtools [05:00:45] Found java - /usr/local/bin/java [05:00:45] Found snpEff - /usr/local/bin/snpEff [05:00:45] Found samclip - /usr/local/bin/samclip [05:00:45] Found seqtk - /usr/local/bin/seqtk [05:00:45] Found parallel - /usr/local/bin/parallel [05:00:45] Found freebayes - /usr/local/bin/freebayes [05:00:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:00:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:00:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:00:45] Found vcfuniq - /usr/local/bin/vcfuniq [05:00:45] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:00:45] Found gzip - /bin/gzip [05:00:45] Found vt - /usr/local/bin/vt [05:00:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:00:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:00:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:00:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:00:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:00:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:00:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:00:46] Please supply a reference FASTA/GBK/EMBL file with --reference
3[05:01:00] This is snippy 4.6.0
Show full stderr[05:01:00] This is snippy 4.6.0 [05:01:00] Written by Torsten Seemann [05:01:00] Obtained from https://github.com/tseemann/snippy [05:01:00] Detected operating system: linux [05:01:00] Enabling bundled linux tools. [05:01:00] Found bwa - /usr/local/bin/bwa [05:01:00] Found bcftools - /usr/local/bin/bcftools [05:01:00] Found samtools - /usr/local/bin/samtools [05:01:00] Found java - /usr/local/bin/java [05:01:00] Found snpEff - /usr/local/bin/snpEff [05:01:00] Found samclip - /usr/local/bin/samclip [05:01:00] Found seqtk - /usr/local/bin/seqtk [05:01:00] Found parallel - /usr/local/bin/parallel [05:01:00] Found freebayes - /usr/local/bin/freebayes [05:01:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:01:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:01:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:01:00] Found vcfuniq - /usr/local/bin/vcfuniq [05:01:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:01:00] Found gzip - /bin/gzip [05:01:00] Found vt - /usr/local/bin/vt [05:01:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:01:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:01:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:01:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:01:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:01:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:01:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:01:01] Please supply a reference FASTA/GBK/EMBL file with --reference
3[05:01:31] This is snippy 4.6.0
Show full stderr[05:01:31] This is snippy 4.6.0 [05:01:31] Written by Torsten Seemann [05:01:31] Obtained from https://github.com/tseemann/snippy [05:01:31] Detected operating system: linux [05:01:31] Enabling bundled linux tools. [05:01:31] Found bwa - /usr/local/bin/bwa [05:01:31] Found bcftools - /usr/local/bin/bcftools [05:01:31] Found samtools - /usr/local/bin/samtools [05:01:31] Found java - /usr/local/bin/java [05:01:31] Found snpEff - /usr/local/bin/snpEff [05:01:31] Found samclip - /usr/local/bin/samclip [05:01:31] Found seqtk - /usr/local/bin/seqtk [05:01:31] Found parallel - /usr/local/bin/parallel [05:01:31] Found freebayes - /usr/local/bin/freebayes [05:01:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:01:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:01:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:01:31] Found vcfuniq - /usr/local/bin/vcfuniq [05:01:31] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:01:31] Found gzip - /bin/gzip [05:01:31] Found vt - /usr/local/bin/vt [05:01:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:01:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:01:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:01:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:01:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:01:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:01:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:01:32] Please supply a reference FASTA/GBK/EMBL file with --reference
3[04:58:54] This is snippy 4.6.0
Show full stderr[04:58:54] This is snippy 4.6.0 [04:58:54] Written by Torsten Seemann [04:58:54] Obtained from https://github.com/tseemann/snippy [04:58:54] Detected operating system: linux [04:58:54] Enabling bundled linux tools. [04:58:54] Found bwa - /usr/local/bin/bwa [04:58:54] Found bcftools - /usr/local/bin/bcftools [04:58:54] Found samtools - /usr/local/bin/samtools [04:58:54] Found java - /usr/local/bin/java [04:58:54] Found snpEff - /usr/local/bin/snpEff [04:58:54] Found samclip - /usr/local/bin/samclip [04:58:54] Found seqtk - /usr/local/bin/seqtk [04:58:54] Found parallel - /usr/local/bin/parallel [04:58:54] Found freebayes - /usr/local/bin/freebayes [04:58:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:58:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:58:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:58:54] Found vcfuniq - /usr/local/bin/vcfuniq [04:58:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:58:54] Found gzip - /bin/gzip [04:58:54] Found vt - /usr/local/bin/vt [04:58:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:58:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:58:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:58:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:58:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:58:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:58:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:58:55] Please supply a reference FASTA/GBK/EMBL file with --reference
3[05:02:08] This is snippy 4.6.0
Show full stderr[05:02:08] This is snippy 4.6.0 [05:02:08] Written by Torsten Seemann [05:02:08] Obtained from https://github.com/tseemann/snippy [05:02:08] Detected operating system: linux [05:02:08] Enabling bundled linux tools. [05:02:08] Found bwa - /usr/local/bin/bwa [05:02:08] Found bcftools - /usr/local/bin/bcftools [05:02:08] Found samtools - /usr/local/bin/samtools [05:02:08] Found java - /usr/local/bin/java [05:02:08] Found snpEff - /usr/local/bin/snpEff [05:02:08] Found samclip - /usr/local/bin/samclip [05:02:08] Found seqtk - /usr/local/bin/seqtk [05:02:08] Found parallel - /usr/local/bin/parallel [05:02:08] Found freebayes - /usr/local/bin/freebayes [05:02:08] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:02:08] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:02:08] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:02:08] Found vcfuniq - /usr/local/bin/vcfuniq [05:02:08] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:02:08] Found gzip - /bin/gzip [05:02:08] Found vt - /usr/local/bin/vt [05:02:08] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:02:08] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:02:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:02:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:02:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:02:09] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:02:09] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:02:09] Please supply a reference FASTA/GBK/EMBL file with --reference
3[05:03:32] This is snippy 4.6.0
Show full stderr[05:03:32] This is snippy 4.6.0 [05:03:32] Written by Torsten Seemann [05:03:32] Obtained from https://github.com/tseemann/snippy [05:03:32] Detected operating system: linux [05:03:32] Enabling bundled linux tools. [05:03:32] Found bwa - /usr/local/bin/bwa [05:03:32] Found bcftools - /usr/local/bin/bcftools [05:03:32] Found samtools - /usr/local/bin/samtools [05:03:32] Found java - /usr/local/bin/java [05:03:32] Found snpEff - /usr/local/bin/snpEff [05:03:32] Found samclip - /usr/local/bin/samclip [05:03:32] Found seqtk - /usr/local/bin/seqtk [05:03:32] Found parallel - /usr/local/bin/parallel [05:03:32] Found freebayes - /usr/local/bin/freebayes [05:03:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:03:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:03:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:03:32] Found vcfuniq - /usr/local/bin/vcfuniq [05:03:32] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:03:32] Found gzip - /bin/gzip [05:03:32] Found vt - /usr/local/bin/vt [05:03:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:03:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:03:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:03:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:03:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:03:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:03:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:03:32] Please supply a reference FASTA/GBK/EMBL file with --reference
3[05:02:34] This is snippy 4.6.0
Show full stderr[05:02:34] This is snippy 4.6.0 [05:02:34] Written by Torsten Seemann [05:02:34] Obtained from https://github.com/tseemann/snippy [05:02:34] Detected operating system: linux [05:02:34] Enabling bundled linux tools. [05:02:34] Found bwa - /usr/local/bin/bwa [05:02:34] Found bcftools - /usr/local/bin/bcftools [05:02:34] Found samtools - /usr/local/bin/samtools [05:02:34] Found java - /usr/local/bin/java [05:02:34] Found snpEff - /usr/local/bin/snpEff [05:02:34] Found samclip - /usr/local/bin/samclip [05:02:35] Found seqtk - /usr/local/bin/seqtk [05:02:35] Found parallel - /usr/local/bin/parallel [05:02:35] Found freebayes - /usr/local/bin/freebayes [05:02:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:02:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:02:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:02:35] Found vcfuniq - /usr/local/bin/vcfuniq [05:02:35] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:02:35] Found gzip - /bin/gzip [05:02:35] Found vt - /usr/local/bin/vt [05:02:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:02:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:02:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:02:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:02:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:02:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:02:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:02:35] Please supply a reference FASTA/GBK/EMBL file with --reference
3[05:04:02] This is snippy 4.6.0
Show full stderr[05:04:02] This is snippy 4.6.0 [05:04:02] Written by Torsten Seemann [05:04:02] Obtained from https://github.com/tseemann/snippy [05:04:02] Detected operating system: linux [05:04:02] Enabling bundled linux tools. [05:04:02] Found bwa - /usr/local/bin/bwa [05:04:02] Found bcftools - /usr/local/bin/bcftools [05:04:02] Found samtools - /usr/local/bin/samtools [05:04:02] Found java - /usr/local/bin/java [05:04:02] Found snpEff - /usr/local/bin/snpEff [05:04:02] Found samclip - /usr/local/bin/samclip [05:04:02] Found seqtk - /usr/local/bin/seqtk [05:04:02] Found parallel - /usr/local/bin/parallel [05:04:02] Found freebayes - /usr/local/bin/freebayes [05:04:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:04:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:04:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:04:02] Found vcfuniq - /usr/local/bin/vcfuniq [05:04:02] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:04:02] Found gzip - /bin/gzip [05:04:02] Found vt - /usr/local/bin/vt [05:04:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:04:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:04:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:04:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:04:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:04:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:04:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:04:03] Please supply a reference FASTA/GBK/EMBL file with --reference
3[05:05:02] This is snippy 4.6.0
Show full stderr[05:05:02] This is snippy 4.6.0 [05:05:02] Written by Torsten Seemann [05:05:02] Obtained from https://github.com/tseemann/snippy [05:05:02] Detected operating system: linux [05:05:02] Enabling bundled linux tools. [05:05:02] Found bwa - /usr/local/bin/bwa [05:05:02] Found bcftools - /usr/local/bin/bcftools [05:05:02] Found samtools - /usr/local/bin/samtools [05:05:02] Found java - /usr/local/bin/java [05:05:02] Found snpEff - /usr/local/bin/snpEff [05:05:02] Found samclip - /usr/local/bin/samclip [05:05:02] Found seqtk - /usr/local/bin/seqtk [05:05:02] Found parallel - /usr/local/bin/parallel [05:05:02] Found freebayes - /usr/local/bin/freebayes [05:05:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:05:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:05:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:05:02] Found vcfuniq - /usr/local/bin/vcfuniq [05:05:02] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:05:02] Found gzip - /bin/gzip [05:05:02] Found vt - /usr/local/bin/vt [05:05:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:05:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:05:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:05:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:05:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:05:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:05:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:05:03] Please supply a reference FASTA/GBK/EMBL file with --reference
3[05:05:36] This is snippy 4.6.0
Show full stderr[05:05:36] This is snippy 4.6.0 [05:05:36] Written by Torsten Seemann [05:05:36] Obtained from https://github.com/tseemann/snippy [05:05:36] Detected operating system: linux [05:05:36] Enabling bundled linux tools. [05:05:36] Found bwa - /usr/local/bin/bwa [05:05:36] Found bcftools - /usr/local/bin/bcftools [05:05:36] Found samtools - /usr/local/bin/samtools [05:05:36] Found java - /usr/local/bin/java [05:05:36] Found snpEff - /usr/local/bin/snpEff [05:05:36] Found samclip - /usr/local/bin/samclip [05:05:36] Found seqtk - /usr/local/bin/seqtk [05:05:36] Found parallel - /usr/local/bin/parallel [05:05:36] Found freebayes - /usr/local/bin/freebayes [05:05:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:05:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:05:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:05:36] Found vcfuniq - /usr/local/bin/vcfuniq [05:05:36] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:05:36] Found gzip - /bin/gzip [05:05:36] Found vt - /usr/local/bin/vt [05:05:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:05:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:05:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:05:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:05:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:05:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:05:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:05:37] Please supply a reference FASTA/GBK/EMBL file with --reference
3[05:05:51] This is snippy 4.6.0
Show full stderr[05:05:51] This is snippy 4.6.0 [05:05:51] Written by Torsten Seemann [05:05:51] Obtained from https://github.com/tseemann/snippy [05:05:51] Detected operating system: linux [05:05:51] Enabling bundled linux tools. [05:05:51] Found bwa - /usr/local/bin/bwa [05:05:51] Found bcftools - /usr/local/bin/bcftools [05:05:51] Found samtools - /usr/local/bin/samtools [05:05:51] Found java - /usr/local/bin/java [05:05:51] Found snpEff - /usr/local/bin/snpEff [05:05:51] Found samclip - /usr/local/bin/samclip [05:05:51] Found seqtk - /usr/local/bin/seqtk [05:05:51] Found parallel - /usr/local/bin/parallel [05:05:51] Found freebayes - /usr/local/bin/freebayes [05:05:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:05:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:05:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:05:51] Found vcfuniq - /usr/local/bin/vcfuniq [05:05:51] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:05:51] Found gzip - /bin/gzip [05:05:51] Found vt - /usr/local/bin/vt [05:05:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:05:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:05:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:05:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:05:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:05:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:05:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:05:52] Please supply a reference FASTA/GBK/EMBL file with --reference
3[05:06:06] This is snippy 4.6.0
Show full stderr[05:06:06] This is snippy 4.6.0 [05:06:06] Written by Torsten Seemann [05:06:06] Obtained from https://github.com/tseemann/snippy [05:06:06] Detected operating system: linux [05:06:06] Enabling bundled linux tools. [05:06:06] Found bwa - /usr/local/bin/bwa [05:06:06] Found bcftools - /usr/local/bin/bcftools [05:06:06] Found samtools - /usr/local/bin/samtools [05:06:06] Found java - /usr/local/bin/java [05:06:06] Found snpEff - /usr/local/bin/snpEff [05:06:06] Found samclip - /usr/local/bin/samclip [05:06:06] Found seqtk - /usr/local/bin/seqtk [05:06:06] Found parallel - /usr/local/bin/parallel [05:06:06] Found freebayes - /usr/local/bin/freebayes [05:06:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:06:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:06:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:06:06] Found vcfuniq - /usr/local/bin/vcfuniq [05:06:06] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:06:06] Found gzip - /bin/gzip [05:06:06] Found vt - /usr/local/bin/vt [05:06:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:06:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:06:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:06:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:06:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:06:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:06:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:06:07] Please supply a reference FASTA/GBK/EMBL file with --reference
3[05:03:47] This is snippy 4.6.0
Show full stderr[05:03:47] This is snippy 4.6.0 [05:03:47] Written by Torsten Seemann [05:03:47] Obtained from https://github.com/tseemann/snippy [05:03:47] Detected operating system: linux [05:03:47] Enabling bundled linux tools. [05:03:47] Found bwa - /usr/local/bin/bwa [05:03:47] Found bcftools - /usr/local/bin/bcftools [05:03:47] Found samtools - /usr/local/bin/samtools [05:03:47] Found java - /usr/local/bin/java [05:03:47] Found snpEff - /usr/local/bin/snpEff [05:03:47] Found samclip - /usr/local/bin/samclip [05:03:47] Found seqtk - /usr/local/bin/seqtk [05:03:47] Found parallel - /usr/local/bin/parallel [05:03:47] Found freebayes - /usr/local/bin/freebayes [05:03:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:03:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:03:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:03:47] Found vcfuniq - /usr/local/bin/vcfuniq [05:03:47] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:03:47] Found gzip - /bin/gzip [05:03:47] Found vt - /usr/local/bin/vt [05:03:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:03:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:03:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:03:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:03:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:03:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:03:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:03:48] Please supply a reference FASTA/GBK/EMBL file with --reference
3[05:07:09] This is snippy 4.6.0
Show full stderr[05:07:09] This is snippy 4.6.0 [05:07:09] Written by Torsten Seemann [05:07:09] Obtained from https://github.com/tseemann/snippy [05:07:09] Detected operating system: linux [05:07:09] Enabling bundled linux tools. [05:07:09] Found bwa - /usr/local/bin/bwa [05:07:09] Found bcftools - /usr/local/bin/bcftools [05:07:09] Found samtools - /usr/local/bin/samtools [05:07:09] Found java - /usr/local/bin/java [05:07:09] Found snpEff - /usr/local/bin/snpEff [05:07:09] Found samclip - /usr/local/bin/samclip [05:07:09] Found seqtk - /usr/local/bin/seqtk [05:07:09] Found parallel - /usr/local/bin/parallel [05:07:09] Found freebayes - /usr/local/bin/freebayes [05:07:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:07:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:07:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:07:09] Found vcfuniq - /usr/local/bin/vcfuniq [05:07:09] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:07:09] Found gzip - /bin/gzip [05:07:09] Found vt - /usr/local/bin/vt [05:07:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:07:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:07:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:07:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:07:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:07:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:07:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:07:10] Please supply a reference FASTA/GBK/EMBL file with --reference
3[05:10:42] This is snippy 4.6.0
Show full stderr[05:10:42] This is snippy 4.6.0 [05:10:42] Written by Torsten Seemann [05:10:42] Obtained from https://github.com/tseemann/snippy [05:10:42] Detected operating system: linux [05:10:42] Enabling bundled linux tools. [05:10:42] Found bwa - /usr/local/bin/bwa [05:10:42] Found bcftools - /usr/local/bin/bcftools [05:10:42] Found samtools - /usr/local/bin/samtools [05:10:42] Found java - /usr/local/bin/java [05:10:42] Found snpEff - /usr/local/bin/snpEff [05:10:42] Found samclip - /usr/local/bin/samclip [05:10:43] Found seqtk - /usr/local/bin/seqtk [05:10:43] Found parallel - /usr/local/bin/parallel [05:10:43] Found freebayes - /usr/local/bin/freebayes [05:10:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:10:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:10:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:10:43] Found vcfuniq - /usr/local/bin/vcfuniq [05:10:43] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:10:43] Found gzip - /bin/gzip [05:10:43] Found vt - /usr/local/bin/vt [05:10:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:10:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:10:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:10:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:10:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:10:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:10:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:10:44] Please supply a reference FASTA/GBK/EMBL file with --reference
3[05:10:54] This is snippy 4.6.0
Show full stderr[05:10:54] This is snippy 4.6.0 [05:10:54] Written by Torsten Seemann [05:10:54] Obtained from https://github.com/tseemann/snippy [05:10:54] Detected operating system: linux [05:10:54] Enabling bundled linux tools. [05:10:54] Found bwa - /usr/local/bin/bwa [05:10:54] Found bcftools - /usr/local/bin/bcftools [05:10:54] Found samtools - /usr/local/bin/samtools [05:10:54] Found java - /usr/local/bin/java [05:10:54] Found snpEff - /usr/local/bin/snpEff [05:10:54] Found samclip - /usr/local/bin/samclip [05:10:54] Found seqtk - /usr/local/bin/seqtk [05:10:54] Found parallel - /usr/local/bin/parallel [05:10:54] Found freebayes - /usr/local/bin/freebayes [05:10:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:10:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:10:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:10:54] Found vcfuniq - /usr/local/bin/vcfuniq [05:10:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:10:54] Found gzip - /bin/gzip [05:10:54] Found vt - /usr/local/bin/vt [05:10:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:10:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:10:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:10:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:10:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:10:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:10:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:10:55] Please supply a reference FASTA/GBK/EMBL file with --reference
3[05:08:24] This is snippy 4.6.0
Show full stderr[05:08:24] This is snippy 4.6.0 [05:08:24] Written by Torsten Seemann [05:08:24] Obtained from https://github.com/tseemann/snippy [05:08:24] Detected operating system: linux [05:08:24] Enabling bundled linux tools. [05:08:24] Found bwa - /usr/local/bin/bwa [05:08:24] Found bcftools - /usr/local/bin/bcftools [05:08:24] Found samtools - /usr/local/bin/samtools [05:08:24] Found java - /usr/local/bin/java [05:08:24] Found snpEff - /usr/local/bin/snpEff [05:08:24] Found samclip - /usr/local/bin/samclip [05:08:24] Found seqtk - /usr/local/bin/seqtk [05:08:24] Found parallel - /usr/local/bin/parallel [05:08:24] Found freebayes - /usr/local/bin/freebayes [05:08:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:08:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:08:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:08:24] Found vcfuniq - /usr/local/bin/vcfuniq [05:08:24] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:08:24] Found gzip - /bin/gzip [05:08:24] Found vt - /usr/local/bin/vt [05:08:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:08:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:08:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:08:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:08:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:08:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:08:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:08:25] Please supply a reference FASTA/GBK/EMBL file with --reference
3[05:09:15] This is snippy 4.6.0
Show full stderr[05:09:15] This is snippy 4.6.0 [05:09:15] Written by Torsten Seemann [05:09:15] Obtained from https://github.com/tseemann/snippy [05:09:15] Detected operating system: linux [05:09:15] Enabling bundled linux tools. [05:09:15] Found bwa - /usr/local/bin/bwa [05:09:15] Found bcftools - /usr/local/bin/bcftools [05:09:15] Found samtools - /usr/local/bin/samtools [05:09:15] Found java - /usr/local/bin/java [05:09:15] Found snpEff - /usr/local/bin/snpEff [05:09:15] Found samclip - /usr/local/bin/samclip [05:09:15] Found seqtk - /usr/local/bin/seqtk [05:09:15] Found parallel - /usr/local/bin/parallel [05:09:15] Found freebayes - /usr/local/bin/freebayes [05:09:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:09:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:09:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:09:15] Found vcfuniq - /usr/local/bin/vcfuniq [05:09:15] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:09:15] Found gzip - /bin/gzip [05:09:15] Found vt - /usr/local/bin/vt [05:09:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:09:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:09:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:09:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:09:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:09:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:09:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:09:16] Please supply a reference FASTA/GBK/EMBL file with --reference
3[05:09:30] This is snippy 4.6.0
Show full stderr[05:09:30] This is snippy 4.6.0 [05:09:30] Written by Torsten Seemann [05:09:30] Obtained from https://github.com/tseemann/snippy [05:09:30] Detected operating system: linux [05:09:30] Enabling bundled linux tools. [05:09:30] Found bwa - /usr/local/bin/bwa [05:09:30] Found bcftools - /usr/local/bin/bcftools [05:09:30] Found samtools - /usr/local/bin/samtools [05:09:30] Found java - /usr/local/bin/java [05:09:30] Found snpEff - /usr/local/bin/snpEff [05:09:30] Found samclip - /usr/local/bin/samclip [05:09:30] Found seqtk - /usr/local/bin/seqtk [05:09:30] Found parallel - /usr/local/bin/parallel [05:09:30] Found freebayes - /usr/local/bin/freebayes [05:09:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:09:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:09:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:09:30] Found vcfuniq - /usr/local/bin/vcfuniq [05:09:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:09:30] Found gzip - /bin/gzip [05:09:30] Found vt - /usr/local/bin/vt [05:09:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:09:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:09:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:09:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:09:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:09:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:09:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:09:31] Please supply a reference FASTA/GBK/EMBL file with --reference
3[05:11:09] This is snippy 4.6.0
Show full stderr[05:11:09] This is snippy 4.6.0 [05:11:09] Written by Torsten Seemann [05:11:09] Obtained from https://github.com/tseemann/snippy [05:11:09] Detected operating system: linux [05:11:09] Enabling bundled linux tools. [05:11:09] Found bwa - /usr/local/bin/bwa [05:11:09] Found bcftools - /usr/local/bin/bcftools [05:11:09] Found samtools - /usr/local/bin/samtools [05:11:09] Found java - /usr/local/bin/java [05:11:10] Found snpEff - /usr/local/bin/snpEff [05:11:10] Found samclip - /usr/local/bin/samclip [05:11:10] Found seqtk - /usr/local/bin/seqtk [05:11:10] Found parallel - /usr/local/bin/parallel [05:11:10] Found freebayes - /usr/local/bin/freebayes [05:11:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:11:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:11:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:11:10] Found vcfuniq - /usr/local/bin/vcfuniq [05:11:10] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:11:10] Found gzip - /bin/gzip [05:11:10] Found vt - /usr/local/bin/vt [05:11:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:11:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:11:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:11:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:11:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:11:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:11:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:11:11] Please supply a reference FASTA/GBK/EMBL file with --reference
3[05:11:27] This is snippy 4.6.0
Show full stderr[05:11:27] This is snippy 4.6.0 [05:11:27] Written by Torsten Seemann [05:11:27] Obtained from https://github.com/tseemann/snippy [05:11:27] Detected operating system: linux [05:11:27] Enabling bundled linux tools. [05:11:27] Found bwa - /usr/local/bin/bwa [05:11:27] Found bcftools - /usr/local/bin/bcftools [05:11:27] Found samtools - /usr/local/bin/samtools [05:11:27] Found java - /usr/local/bin/java [05:11:27] Found snpEff - /usr/local/bin/snpEff [05:11:27] Found samclip - /usr/local/bin/samclip [05:11:27] Found seqtk - /usr/local/bin/seqtk [05:11:27] Found parallel - /usr/local/bin/parallel [05:11:27] Found freebayes - /usr/local/bin/freebayes [05:11:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:11:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:11:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:11:27] Found vcfuniq - /usr/local/bin/vcfuniq [05:11:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:11:27] Found gzip - /bin/gzip [05:11:27] Found vt - /usr/local/bin/vt [05:11:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:11:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:11:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:11:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:11:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:11:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:11:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:11:28] Please supply a reference FASTA/GBK/EMBL file with --reference
3[03:40:28] This is snippy 4.6.0
Show full stderr[03:40:28] This is snippy 4.6.0 [03:40:28] Written by Torsten Seemann [03:40:28] Obtained from https://github.com/tseemann/snippy [03:40:28] Detected operating system: linux [03:40:28] Enabling bundled linux tools. [03:40:28] Found bwa - /usr/local/bin/bwa [03:40:28] Found bcftools - /usr/local/bin/bcftools [03:40:28] Found samtools - /usr/local/bin/samtools [03:40:28] Found java - /usr/local/bin/java [03:40:28] Found snpEff - /usr/local/bin/snpEff [03:40:28] Found samclip - /usr/local/bin/samclip [03:40:28] Found seqtk - /usr/local/bin/seqtk [03:40:28] Found parallel - /usr/local/bin/parallel [03:40:28] Found freebayes - /usr/local/bin/freebayes [03:40:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:40:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:40:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:40:28] Found vcfuniq - /usr/local/bin/vcfuniq [03:40:28] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:40:28] Found gzip - /bin/gzip [03:40:28] Found vt - /usr/local/bin/vt [03:40:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:40:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:40:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:40:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:40:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:40:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:40:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:40:29] Please supply a reference FASTA/GBK/EMBL file with --reference
3[03:40:43] This is snippy 4.6.0
Show full stderr[03:40:43] This is snippy 4.6.0 [03:40:43] Written by Torsten Seemann [03:40:43] Obtained from https://github.com/tseemann/snippy [03:40:43] Detected operating system: linux [03:40:43] Enabling bundled linux tools. [03:40:43] Found bwa - /usr/local/bin/bwa [03:40:43] Found bcftools - /usr/local/bin/bcftools [03:40:43] Found samtools - /usr/local/bin/samtools [03:40:43] Found java - /usr/local/bin/java [03:40:43] Found snpEff - /usr/local/bin/snpEff [03:40:43] Found samclip - /usr/local/bin/samclip [03:40:43] Found seqtk - /usr/local/bin/seqtk [03:40:43] Found parallel - /usr/local/bin/parallel [03:40:43] Found freebayes - /usr/local/bin/freebayes [03:40:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:40:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:40:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:40:43] Found vcfuniq - /usr/local/bin/vcfuniq [03:40:43] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:40:43] Found gzip - /bin/gzip [03:40:43] Found vt - /usr/local/bin/vt [03:40:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:40:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:40:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:40:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:40:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:40:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:40:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:40:44] Please supply a reference FASTA/GBK/EMBL file with --reference
3[03:41:14] This is snippy 4.6.0
Show full stderr[03:41:14] This is snippy 4.6.0 [03:41:14] Written by Torsten Seemann [03:41:14] Obtained from https://github.com/tseemann/snippy [03:41:14] Detected operating system: linux [03:41:14] Enabling bundled linux tools. [03:41:14] Found bwa - /usr/local/bin/bwa [03:41:14] Found bcftools - /usr/local/bin/bcftools [03:41:14] Found samtools - /usr/local/bin/samtools [03:41:14] Found java - /usr/local/bin/java [03:41:14] Found snpEff - /usr/local/bin/snpEff [03:41:14] Found samclip - /usr/local/bin/samclip [03:41:14] Found seqtk - /usr/local/bin/seqtk [03:41:14] Found parallel - /usr/local/bin/parallel [03:41:14] Found freebayes - /usr/local/bin/freebayes [03:41:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:41:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:41:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:41:14] Found vcfuniq - /usr/local/bin/vcfuniq [03:41:14] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:41:14] Found gzip - /bin/gzip [03:41:14] Found vt - /usr/local/bin/vt [03:41:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:41:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:41:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:41:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:41:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:41:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:41:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:41:15] Please supply a reference FASTA/GBK/EMBL file with --reference
3[03:41:07] This is snippy 4.6.0
Show full stderr[03:41:07] This is snippy 4.6.0 [03:41:07] Written by Torsten Seemann [03:41:07] Obtained from https://github.com/tseemann/snippy [03:41:07] Detected operating system: linux [03:41:07] Enabling bundled linux tools. [03:41:07] Found bwa - /usr/local/bin/bwa [03:41:07] Found bcftools - /usr/local/bin/bcftools [03:41:07] Found samtools - /usr/local/bin/samtools [03:41:07] Found java - /usr/local/bin/java [03:41:07] Found snpEff - /usr/local/bin/snpEff [03:41:07] Found samclip - /usr/local/bin/samclip [03:41:07] Found seqtk - /usr/local/bin/seqtk [03:41:07] Found parallel - /usr/local/bin/parallel [03:41:07] Found freebayes - /usr/local/bin/freebayes [03:41:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:41:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:41:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:41:07] Found vcfuniq - /usr/local/bin/vcfuniq [03:41:07] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:41:07] Found gzip - /bin/gzip [03:41:07] Found vt - /usr/local/bin/vt [03:41:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:41:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:41:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:41:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:41:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:41:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:41:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:41:08] Please supply a reference FASTA/GBK/EMBL file with --reference
3[03:41:24] This is snippy 4.6.0
Show full stderr[03:41:24] This is snippy 4.6.0 [03:41:24] Written by Torsten Seemann [03:41:24] Obtained from https://github.com/tseemann/snippy [03:41:24] Detected operating system: linux [03:41:24] Enabling bundled linux tools. [03:41:24] Found bwa - /usr/local/bin/bwa [03:41:24] Found bcftools - /usr/local/bin/bcftools [03:41:24] Found samtools - /usr/local/bin/samtools [03:41:24] Found java - /usr/local/bin/java [03:41:24] Found snpEff - /usr/local/bin/snpEff [03:41:24] Found samclip - /usr/local/bin/samclip [03:41:24] Found seqtk - /usr/local/bin/seqtk [03:41:24] Found parallel - /usr/local/bin/parallel [03:41:24] Found freebayes - /usr/local/bin/freebayes [03:41:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:41:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:41:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:41:24] Found vcfuniq - /usr/local/bin/vcfuniq [03:41:24] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:41:24] Found gzip - /bin/gzip [03:41:24] Found vt - /usr/local/bin/vt [03:41:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:41:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:41:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:41:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:41:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:41:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:41:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:41:25] Please supply a reference FASTA/GBK/EMBL file with --reference
3[03:40:13] This is snippy 4.6.0
Show full stderr[03:40:13] This is snippy 4.6.0 [03:40:13] Written by Torsten Seemann [03:40:13] Obtained from https://github.com/tseemann/snippy [03:40:13] Detected operating system: linux [03:40:13] Enabling bundled linux tools. [03:40:13] Found bwa - /usr/local/bin/bwa [03:40:13] Found bcftools - /usr/local/bin/bcftools [03:40:13] Found samtools - /usr/local/bin/samtools [03:40:13] Found java - /usr/local/bin/java [03:40:13] Found snpEff - /usr/local/bin/snpEff [03:40:13] Found samclip - /usr/local/bin/samclip [03:40:13] Found seqtk - /usr/local/bin/seqtk [03:40:13] Found parallel - /usr/local/bin/parallel [03:40:13] Found freebayes - /usr/local/bin/freebayes [03:40:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:40:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:40:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:40:13] Found vcfuniq - /usr/local/bin/vcfuniq [03:40:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:40:13] Found gzip - /bin/gzip [03:40:13] Found vt - /usr/local/bin/vt [03:40:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:40:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:40:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:40:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:40:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:40:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:40:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:40:14] Please supply a reference FASTA/GBK/EMBL file with --reference
3[05:58:25] This is snippy 4.6.0
Show full stderr[05:58:25] This is snippy 4.6.0 [05:58:25] Written by Torsten Seemann [05:58:25] Obtained from https://github.com/tseemann/snippy [05:58:25] Detected operating system: linux [05:58:25] Enabling bundled linux tools. [05:58:25] Found bwa - /usr/local/bin/bwa [05:58:25] Found bcftools - /usr/local/bin/bcftools [05:58:25] Found samtools - /usr/local/bin/samtools [05:58:25] Found java - /usr/local/bin/java [05:58:25] Found snpEff - /usr/local/bin/snpEff [05:58:25] Found samclip - /usr/local/bin/samclip [05:58:26] Found seqtk - /usr/local/bin/seqtk [05:58:26] Found parallel - /usr/local/bin/parallel [05:58:26] Found freebayes - /usr/local/bin/freebayes [05:58:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:58:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:58:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:58:26] Found vcfuniq - /usr/local/bin/vcfuniq [05:58:26] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:58:26] Found gzip - /bin/gzip [05:58:26] Found vt - /usr/local/bin/vt [05:58:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:58:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:58:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:58:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:58:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:58:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:58:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:58:27] Using reference: /cvmfs/data.galaxyproject.org/byhand/microbes/eschColi_APEC_O1/seq/eschColi_APEC_O1.fa [05:58:27] Treating reference as 'fasta' format. [05:58:27] Will use 1 CPU cores. [05:58:27] Using read file: /corral4/main/objects/1/9/a/dataset_19a2fd78-e44a-4c3a-9cb2-f1bf03568361.dat [05:58:27] Creating folder: Resistance_67_fasta [05:58:27] Changing working directory: Resistance_67_fasta [05:58:27] Creating reference folder: reference [05:58:27] Extracting FASTA and GFF from reference. [05:58:27] Wrote 3 sequences to ref.fa [05:58:27] Wrote 0 features to ref.gff [05:58:27] Shredding /corral4/main/objects/1/9/a/dataset_19a2fd78-e44a-4c3a-9cb2-f1bf03568361.dat into pseudo-reads [05:58:31] Wrote 404330 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [05:58:31] Freebayes will process 1 chunks of 5589314 bp, 1 chunks at a time. [05:58:31] Using BAM RG (Read Group) ID: Resistance_67_fasta [05:58:31] Running: samtools faidx reference/ref.fa 2>> snps.log [05:58:31] Running: bwa index reference/ref.fa 2>> snps.log [05:58:37] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [05:58:37] Running: ln -sf reference/ref.fa . 2>> snps.log [05:58:37] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [05:58:37] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [05:58:37] Running: bwa mem -Y -M -R '@RG\tID:Resistance_67_fasta\tSM:Resistance_67_fasta' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/258/72258620/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/258/72258620/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/258/72258620/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 3 sequences in reference/ref.fa.fai
3[05:59:37] This is snippy 4.6.0
Show full stderr[05:59:37] This is snippy 4.6.0 [05:59:37] Written by Torsten Seemann [05:59:37] Obtained from https://github.com/tseemann/snippy [05:59:37] Detected operating system: linux [05:59:37] Enabling bundled linux tools. [05:59:37] Found bwa - /usr/local/bin/bwa [05:59:37] Found bcftools - /usr/local/bin/bcftools [05:59:37] Found samtools - /usr/local/bin/samtools [05:59:37] Found java - /usr/local/bin/java [05:59:37] Found snpEff - /usr/local/bin/snpEff [05:59:37] Found samclip - /usr/local/bin/samclip [05:59:37] Found seqtk - /usr/local/bin/seqtk [05:59:37] Found parallel - /usr/local/bin/parallel [05:59:37] Found freebayes - /usr/local/bin/freebayes [05:59:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:59:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:59:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:59:37] Found vcfuniq - /usr/local/bin/vcfuniq [05:59:37] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:59:37] Found gzip - /bin/gzip [05:59:37] Found vt - /usr/local/bin/vt [05:59:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:59:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:59:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:59:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:59:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:59:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:59:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:59:38] Using reference: /cvmfs/data.galaxyproject.org/byhand/microbes/eschColi_APEC_O1/seq/eschColi_APEC_O1.fa [05:59:38] Treating reference as 'fasta' format. [05:59:38] Will use 1 CPU cores. [05:59:38] Using read file: /corral4/main/objects/2/d/4/dataset_2d4b0322-be49-468a-8c39-1a7e461cee61.dat [05:59:38] Creating folder: Resistance_78_fasta [05:59:38] Changing working directory: Resistance_78_fasta [05:59:38] Creating reference folder: reference [05:59:38] Extracting FASTA and GFF from reference. [05:59:39] Wrote 3 sequences to ref.fa [05:59:39] Wrote 0 features to ref.gff [05:59:39] Shredding /corral4/main/objects/2/d/4/dataset_2d4b0322-be49-468a-8c39-1a7e461cee61.dat into pseudo-reads [05:59:40] Wrote 423200 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [05:59:40] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time. [05:59:40] Using BAM RG (Read Group) ID: Resistance_78_fasta [05:59:40] Running: samtools faidx reference/ref.fa 2>> snps.log [05:59:40] Error running command, check Resistance_78_fasta/snps.log
3[05:57:50] This is snippy 4.6.0
Show full stderr[05:57:50] This is snippy 4.6.0 [05:57:50] Written by Torsten Seemann [05:57:50] Obtained from https://github.com/tseemann/snippy [05:57:50] Detected operating system: linux [05:57:50] Enabling bundled linux tools. [05:57:50] Found bwa - /usr/local/bin/bwa [05:57:50] Found bcftools - /usr/local/bin/bcftools [05:57:50] Found samtools - /usr/local/bin/samtools [05:57:50] Found java - /usr/local/bin/java [05:57:50] Found snpEff - /usr/local/bin/snpEff [05:57:50] Found samclip - /usr/local/bin/samclip [05:57:50] Found seqtk - /usr/local/bin/seqtk [05:57:50] Found parallel - /usr/local/bin/parallel [05:57:50] Found freebayes - /usr/local/bin/freebayes [05:57:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:57:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:57:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:57:50] Found vcfuniq - /usr/local/bin/vcfuniq [05:57:50] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:57:50] Found gzip - /bin/gzip [05:57:50] Found vt - /usr/local/bin/vt [05:57:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:57:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:57:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:57:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:57:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:57:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:57:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:57:51] Using reference: /cvmfs/data.galaxyproject.org/byhand/microbes/eschColi_APEC_O1/seq/eschColi_APEC_O1.fa [05:57:51] Treating reference as 'fasta' format. [05:57:51] Will use 1 CPU cores. [05:57:51] Using read file: /corral4/main/objects/e/9/1/dataset_e91bfa5f-8990-48f6-be27-b003cd51f67b.dat [05:57:51] Creating folder: Resistance_91_fasta [05:57:51] Changing working directory: Resistance_91_fasta [05:57:51] Creating reference folder: reference [05:57:51] Extracting FASTA and GFF from reference. [05:57:51] Wrote 3 sequences to ref.fa [05:57:51] Wrote 0 features to ref.gff [05:57:51] Shredding /corral4/main/objects/e/9/1/dataset_e91bfa5f-8990-48f6-be27-b003cd51f67b.dat into pseudo-reads [05:57:56] Wrote 408646 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [05:57:56] Freebayes will process 1 chunks of 5589314 bp, 1 chunks at a time. [05:57:56] Using BAM RG (Read Group) ID: Resistance_91_fasta [05:57:56] Running: samtools faidx reference/ref.fa 2>> snps.log [05:57:56] Running: bwa index reference/ref.fa 2>> snps.log [05:58:01] Error running command, check Resistance_91_fasta/snps.log
3[06:00:38] This is snippy 4.6.0
Show full stderr[06:00:38] This is snippy 4.6.0 [06:00:38] Written by Torsten Seemann [06:00:38] Obtained from https://github.com/tseemann/snippy [06:00:38] Detected operating system: linux [06:00:38] Enabling bundled linux tools. [06:00:38] Found bwa - /usr/local/bin/bwa [06:00:38] Found bcftools - /usr/local/bin/bcftools [06:00:38] Found samtools - /usr/local/bin/samtools [06:00:38] Found java - /usr/local/bin/java [06:00:38] Found snpEff - /usr/local/bin/snpEff [06:00:38] Found samclip - /usr/local/bin/samclip [06:00:38] Found seqtk - /usr/local/bin/seqtk [06:00:38] Found parallel - /usr/local/bin/parallel [06:00:38] Found freebayes - /usr/local/bin/freebayes [06:00:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:00:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:00:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:00:38] Found vcfuniq - /usr/local/bin/vcfuniq [06:00:38] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:00:38] Found gzip - /bin/gzip [06:00:38] Found vt - /usr/local/bin/vt [06:00:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:00:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:00:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:00:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:00:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:00:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:00:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:00:39] Using reference: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat [06:00:39] Treating reference as 'fasta' format. [06:00:39] Will use 1 CPU cores. [06:00:39] Using read file: /corral4/main/objects/6/2/a/dataset_62a43897-e30a-4af9-a292-edd238d278b3.dat [06:00:39] Creating folder: GCF_905183075_1_MAF65v1_genomic_fna [06:00:39] Changing working directory: GCF_905183075_1_MAF65v1_genomic_fna [06:00:39] Creating reference folder: reference [06:00:39] Extracting FASTA and GFF from reference. [06:00:40] Wrote 1 sequences to ref.fa [06:00:40] Wrote 0 features to ref.gff [06:00:40] Shredding /corral4/main/objects/6/2/a/dataset_62a43897-e30a-4af9-a292-edd238d278b3.dat into pseudo-reads [06:00:43] Wrote 350040 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [06:00:43] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time. [06:00:43] Using BAM RG (Read Group) ID: GCF_905183075_1_MAF65v1_genomic_fna [06:00:43] Running: samtools faidx reference/ref.fa 2>> snps.log [06:00:44] Error running command, check GCF_905183075_1_MAF65v1_genomic_fna/snps.log
3[07:04:40] This is snippy 4.6.0
Show full stderr[07:04:40] This is snippy 4.6.0 [07:04:40] Written by Torsten Seemann [07:04:40] Obtained from https://github.com/tseemann/snippy [07:04:40] Detected operating system: linux [07:04:40] Enabling bundled linux tools. [07:04:40] Found bwa - /usr/local/bin/bwa [07:04:40] Found bcftools - /usr/local/bin/bcftools [07:04:40] Found samtools - /usr/local/bin/samtools [07:04:40] Found java - /usr/local/bin/java [07:04:40] Found snpEff - /usr/local/bin/snpEff [07:04:40] Found samclip - /usr/local/bin/samclip [07:04:40] Found seqtk - /usr/local/bin/seqtk [07:04:40] Found parallel - /usr/local/bin/parallel [07:04:40] Found freebayes - /usr/local/bin/freebayes [07:04:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:04:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:04:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:04:40] Found vcfuniq - /usr/local/bin/vcfuniq [07:04:40] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:04:40] Found gzip - /bin/gzip [07:04:40] Found vt - /usr/local/bin/vt [07:04:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:04:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:04:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:04:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:04:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:04:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:04:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:04:41] Using reference: /corral4/main/objects/b/c/7/dataset_bc72f994-0ee8-49f5-b32a-d0eb5858fef9.dat [07:04:41] Treating reference as 'fasta' format. [07:04:41] Will use 1 CPU cores. [07:04:41] Using read file: /corral4/main/objects/b/9/3/dataset_b931e0c8-c97a-491e-9665-7515b51f803c.dat [07:04:41] Creating folder: BVBRC_genome_sequence___2025_10_25T135701_613_fasta [07:04:41] Changing working directory: BVBRC_genome_sequence___2025_10_25T135701_613_fasta [07:04:41] Creating reference folder: reference [07:04:41] Extracting FASTA and GFF from reference. [07:04:41] Wrote 1 sequences to ref.fa [07:04:41] Wrote 0 features to ref.gff [07:04:41] Shredding /corral4/main/objects/b/9/3/dataset_b931e0c8-c97a-491e-9665-7515b51f803c.dat into pseudo-reads [07:04:43] Wrote 219280 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [07:04:43] Freebayes will process 1 chunks of 2868471 bp, 1 chunks at a time. [07:04:43] Using BAM RG (Read Group) ID: BVBRC_genome_sequence___2025_10_25T135701_613_fasta [07:04:43] Running: samtools faidx reference/ref.fa 2>> snps.log [07:04:43] Running: bwa index reference/ref.fa 2>> snps.log [07:04:45] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [07:04:45] Running: ln -sf reference/ref.fa . 2>> snps.log [07:04:45] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [07:04:45] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [07:04:45] Running: bwa mem -Y -M -R '@RG\tID:BVBRC_genome_sequence___2025_10_25T135701_613_fasta\tSM:BVBRC_genome_sequence___2025_10_25T135701_613_fasta' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/261/72261362/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/261/72261362/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/261/72261362/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samcl
3[07:06:19] This is snippy 4.6.0
Show full stderr[07:06:19] This is snippy 4.6.0 [07:06:19] Written by Torsten Seemann [07:06:19] Obtained from https://github.com/tseemann/snippy [07:06:19] Detected operating system: linux [07:06:19] Enabling bundled linux tools. [07:06:19] Found bwa - /usr/local/bin/bwa [07:06:19] Found bcftools - /usr/local/bin/bcftools [07:06:19] Found samtools - /usr/local/bin/samtools [07:06:19] Found java - /usr/local/bin/java [07:06:19] Found snpEff - /usr/local/bin/snpEff [07:06:19] Found samclip - /usr/local/bin/samclip [07:06:19] Found seqtk - /usr/local/bin/seqtk [07:06:19] Found parallel - /usr/local/bin/parallel [07:06:19] Found freebayes - /usr/local/bin/freebayes [07:06:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:06:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:06:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:06:19] Found vcfuniq - /usr/local/bin/vcfuniq [07:06:19] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:06:19] Found gzip - /bin/gzip [07:06:19] Found vt - /usr/local/bin/vt [07:06:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:06:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:06:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:06:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:06:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:06:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:06:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:06:20] Using reference: /corral4/main/objects/b/c/7/dataset_bc72f994-0ee8-49f5-b32a-d0eb5858fef9.dat [07:06:20] Treating reference as 'fasta' format. [07:06:20] Will use 1 CPU cores. [07:06:20] Using read file: /corral4/main/objects/0/6/9/dataset_06964298-cc9f-4687-8505-bd01ff7cfad2.dat [07:06:20] Creating folder: BVBRC_genome_sequence___2025_10_25T135853_778_fasta [07:06:20] Changing working directory: BVBRC_genome_sequence___2025_10_25T135853_778_fasta [07:06:20] Creating reference folder: reference [07:06:20] Extracting FASTA and GFF from reference. [07:06:20] Wrote 1 sequences to ref.fa [07:06:20] Wrote 0 features to ref.gff [07:06:20] Shredding /corral4/main/objects/0/6/9/dataset_06964298-cc9f-4687-8505-bd01ff7cfad2.dat into pseudo-reads [07:06:22] Wrote 225244 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [07:06:22] Freebayes will process 1 chunks of 2868471 bp, 1 chunks at a time. [07:06:22] Using BAM RG (Read Group) ID: BVBRC_genome_sequence___2025_10_25T135853_778_fasta [07:06:22] Running: samtools faidx reference/ref.fa 2>> snps.log [07:06:23] Running: bwa index reference/ref.fa 2>> snps.log [07:06:23] Error running command, check BVBRC_genome_sequence___2025_10_25T135853_778_fasta/snps.log
3[06:48:27] This is snippy 4.6.0
Show full stderr[06:48:27] This is snippy 4.6.0 [06:48:27] Written by Torsten Seemann [06:48:27] Obtained from https://github.com/tseemann/snippy [06:48:27] Detected operating system: linux [06:48:27] Enabling bundled linux tools. [06:48:27] Found bwa - /usr/local/bin/bwa [06:48:27] Found bcftools - /usr/local/bin/bcftools [06:48:27] Found samtools - /usr/local/bin/samtools [06:48:27] Found java - /usr/local/bin/java [06:48:27] Found snpEff - /usr/local/bin/snpEff [06:48:27] Found samclip - /usr/local/bin/samclip [06:48:27] Found seqtk - /usr/local/bin/seqtk [06:48:27] Found parallel - /usr/local/bin/parallel [06:48:27] Found freebayes - /usr/local/bin/freebayes [06:48:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:48:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:48:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:48:27] Found vcfuniq - /usr/local/bin/vcfuniq [06:48:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:48:27] Found gzip - /bin/gzip [06:48:27] Found vt - /usr/local/bin/vt [06:48:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:48:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:48:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:48:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:48:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:48:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:48:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:48:28] Please supply a reference FASTA/GBK/EMBL file with --reference
3[07:07:13] This is snippy 4.6.0
Show full stderr[07:07:13] This is snippy 4.6.0 [07:07:13] Written by Torsten Seemann [07:07:13] Obtained from https://github.com/tseemann/snippy [07:07:13] Detected operating system: linux [07:07:13] Enabling bundled linux tools. [07:07:13] Found bwa - /usr/local/bin/bwa [07:07:13] Found bcftools - /usr/local/bin/bcftools [07:07:13] Found samtools - /usr/local/bin/samtools [07:07:13] Found java - /usr/local/bin/java [07:07:13] Found snpEff - /usr/local/bin/snpEff [07:07:13] Found samclip - /usr/local/bin/samclip [07:07:13] Found seqtk - /usr/local/bin/seqtk [07:07:13] Found parallel - /usr/local/bin/parallel [07:07:13] Found freebayes - /usr/local/bin/freebayes [07:07:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:07:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:07:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:07:13] Found vcfuniq - /usr/local/bin/vcfuniq [07:07:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:07:13] Found gzip - /bin/gzip [07:07:13] Found vt - /usr/local/bin/vt [07:07:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:07:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:07:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:07:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:07:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:07:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:07:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:07:14] Please supply a reference FASTA/GBK/EMBL file with --reference
3[06:48:14] This is snippy 4.6.0
Show full stderr[06:48:14] This is snippy 4.6.0 [06:48:14] Written by Torsten Seemann [06:48:14] Obtained from https://github.com/tseemann/snippy [06:48:14] Detected operating system: linux [06:48:14] Enabling bundled linux tools. [06:48:14] Found bwa - /usr/local/bin/bwa [06:48:14] Found bcftools - /usr/local/bin/bcftools [06:48:14] Found samtools - /usr/local/bin/samtools [06:48:14] Found java - /usr/local/bin/java [06:48:14] Found snpEff - /usr/local/bin/snpEff [06:48:14] Found samclip - /usr/local/bin/samclip [06:48:14] Found seqtk - /usr/local/bin/seqtk [06:48:14] Found parallel - /usr/local/bin/parallel [06:48:14] Found freebayes - /usr/local/bin/freebayes [06:48:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:48:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:48:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:48:14] Found vcfuniq - /usr/local/bin/vcfuniq [06:48:14] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:48:14] Found gzip - /bin/gzip [06:48:14] Found vt - /usr/local/bin/vt [06:48:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:48:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:48:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:48:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:48:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:48:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:48:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:48:15] Please supply a reference FASTA/GBK/EMBL file with --reference
3[06:54:00] This is snippy 4.6.0
Show full stderr[06:54:00] This is snippy 4.6.0 [06:54:00] Written by Torsten Seemann [06:54:00] Obtained from https://github.com/tseemann/snippy [06:54:00] Detected operating system: linux [06:54:00] Enabling bundled linux tools. [06:54:00] Found bwa - /usr/local/bin/bwa [06:54:00] Found bcftools - /usr/local/bin/bcftools [06:54:00] Found samtools - /usr/local/bin/samtools [06:54:00] Found java - /usr/local/bin/java [06:54:00] Found snpEff - /usr/local/bin/snpEff [06:54:00] Found samclip - /usr/local/bin/samclip [06:54:00] Found seqtk - /usr/local/bin/seqtk [06:54:00] Found parallel - /usr/local/bin/parallel [06:54:00] Found freebayes - /usr/local/bin/freebayes [06:54:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:54:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:54:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:54:00] Found vcfuniq - /usr/local/bin/vcfuniq [06:54:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:54:00] Found gzip - /bin/gzip [06:54:00] Found vt - /usr/local/bin/vt [06:54:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:54:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:54:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:54:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:54:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:54:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:54:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:54:01] Please supply a reference FASTA/GBK/EMBL file with --reference
3[06:49:48] This is snippy 4.6.0
Show full stderr[06:49:48] This is snippy 4.6.0 [06:49:48] Written by Torsten Seemann [06:49:48] Obtained from https://github.com/tseemann/snippy [06:49:48] Detected operating system: linux [06:49:48] Enabling bundled linux tools. [06:49:48] Found bwa - /usr/local/bin/bwa [06:49:48] Found bcftools - /usr/local/bin/bcftools [06:49:48] Found samtools - /usr/local/bin/samtools [06:49:48] Found java - /usr/local/bin/java [06:49:48] Found snpEff - /usr/local/bin/snpEff [06:49:48] Found samclip - /usr/local/bin/samclip [06:49:48] Found seqtk - /usr/local/bin/seqtk [06:49:48] Found parallel - /usr/local/bin/parallel [06:49:48] Found freebayes - /usr/local/bin/freebayes [06:49:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:49:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:49:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:49:48] Found vcfuniq - /usr/local/bin/vcfuniq [06:49:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:49:48] Found gzip - /bin/gzip [06:49:48] Found vt - /usr/local/bin/vt [06:49:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:49:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:49:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:49:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:49:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:49:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:49:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:49:49] Please supply a reference FASTA/GBK/EMBL file with --reference
3[06:50:00] This is snippy 4.6.0
Show full stderr[06:50:00] This is snippy 4.6.0 [06:50:00] Written by Torsten Seemann [06:50:00] Obtained from https://github.com/tseemann/snippy [06:50:00] Detected operating system: linux [06:50:00] Enabling bundled linux tools. [06:50:00] Found bwa - /usr/local/bin/bwa [06:50:00] Found bcftools - /usr/local/bin/bcftools [06:50:00] Found samtools - /usr/local/bin/samtools [06:50:00] Found java - /usr/local/bin/java [06:50:00] Found snpEff - /usr/local/bin/snpEff [06:50:00] Found samclip - /usr/local/bin/samclip [06:50:00] Found seqtk - /usr/local/bin/seqtk [06:50:00] Found parallel - /usr/local/bin/parallel [06:50:00] Found freebayes - /usr/local/bin/freebayes [06:50:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:50:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:50:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:50:00] Found vcfuniq - /usr/local/bin/vcfuniq [06:50:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:50:00] Found gzip - /bin/gzip [06:50:00] Found vt - /usr/local/bin/vt [06:50:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:50:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:50:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:50:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:50:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:50:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:50:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:50:01] Please supply a reference FASTA/GBK/EMBL file with --reference
3[07:31:47] This is snippy 4.6.0
Show full stderr[07:31:47] This is snippy 4.6.0 [07:31:47] Written by Torsten Seemann [07:31:47] Obtained from https://github.com/tseemann/snippy [07:31:47] Detected operating system: linux [07:31:47] Enabling bundled linux tools. [07:31:47] Found bwa - /usr/local/bin/bwa [07:31:47] Found bcftools - /usr/local/bin/bcftools [07:31:47] Found samtools - /usr/local/bin/samtools [07:31:47] Found java - /usr/local/bin/java [07:31:47] Found snpEff - /usr/local/bin/snpEff [07:31:47] Found samclip - /usr/local/bin/samclip [07:31:47] Found seqtk - /usr/local/bin/seqtk [07:31:47] Found parallel - /usr/local/bin/parallel [07:31:47] Found freebayes - /usr/local/bin/freebayes [07:31:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:31:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:31:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:31:47] Found vcfuniq - /usr/local/bin/vcfuniq [07:31:47] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:31:47] Found gzip - /bin/gzip [07:31:47] Found vt - /usr/local/bin/vt [07:31:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:31:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:31:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:31:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:31:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:31:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:31:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:31:48] Please supply a reference FASTA/GBK/EMBL file with --reference
3[07:38:10] This is snippy 4.6.0
Show full stderr[07:38:10] This is snippy 4.6.0 [07:38:10] Written by Torsten Seemann [07:38:10] Obtained from https://github.com/tseemann/snippy [07:38:10] Detected operating system: linux [07:38:10] Enabling bundled linux tools. [07:38:10] Found bwa - /usr/local/bin/bwa [07:38:10] Found bcftools - /usr/local/bin/bcftools [07:38:10] Found samtools - /usr/local/bin/samtools [07:38:10] Found java - /usr/local/bin/java [07:38:10] Found snpEff - /usr/local/bin/snpEff [07:38:10] Found samclip - /usr/local/bin/samclip [07:38:10] Found seqtk - /usr/local/bin/seqtk [07:38:10] Found parallel - /usr/local/bin/parallel [07:38:10] Found freebayes - /usr/local/bin/freebayes [07:38:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:38:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:38:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:38:10] Found vcfuniq - /usr/local/bin/vcfuniq [07:38:10] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:38:10] Found gzip - /bin/gzip [07:38:10] Found vt - /usr/local/bin/vt [07:38:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:38:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:38:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:38:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:38:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:38:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:38:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:38:11] Please supply a reference FASTA/GBK/EMBL file with --reference
3[06:50:13] This is snippy 4.6.0
Show full stderr[06:50:13] This is snippy 4.6.0 [06:50:13] Written by Torsten Seemann [06:50:13] Obtained from https://github.com/tseemann/snippy [06:50:13] Detected operating system: linux [06:50:13] Enabling bundled linux tools. [06:50:13] Found bwa - /usr/local/bin/bwa [06:50:13] Found bcftools - /usr/local/bin/bcftools [06:50:13] Found samtools - /usr/local/bin/samtools [06:50:13] Found java - /usr/local/bin/java [06:50:13] Found snpEff - /usr/local/bin/snpEff [06:50:13] Found samclip - /usr/local/bin/samclip [06:50:13] Found seqtk - /usr/local/bin/seqtk [06:50:13] Found parallel - /usr/local/bin/parallel [06:50:13] Found freebayes - /usr/local/bin/freebayes [06:50:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:50:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:50:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:50:13] Found vcfuniq - /usr/local/bin/vcfuniq [06:50:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:50:13] Found gzip - /bin/gzip [06:50:13] Found vt - /usr/local/bin/vt [06:50:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:50:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:50:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:50:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:50:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:50:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:50:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:50:14] Please supply a reference FASTA/GBK/EMBL file with --reference
3[06:50:25] This is snippy 4.6.0
Show full stderr[06:50:25] This is snippy 4.6.0 [06:50:25] Written by Torsten Seemann [06:50:25] Obtained from https://github.com/tseemann/snippy [06:50:25] Detected operating system: linux [06:50:25] Enabling bundled linux tools. [06:50:25] Found bwa - /usr/local/bin/bwa [06:50:25] Found bcftools - /usr/local/bin/bcftools [06:50:25] Found samtools - /usr/local/bin/samtools [06:50:25] Found java - /usr/local/bin/java [06:50:25] Found snpEff - /usr/local/bin/snpEff [06:50:25] Found samclip - /usr/local/bin/samclip [06:50:25] Found seqtk - /usr/local/bin/seqtk [06:50:25] Found parallel - /usr/local/bin/parallel [06:50:25] Found freebayes - /usr/local/bin/freebayes [06:50:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:50:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:50:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:50:25] Found vcfuniq - /usr/local/bin/vcfuniq [06:50:25] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:50:25] Found gzip - /bin/gzip [06:50:25] Found vt - /usr/local/bin/vt [06:50:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:50:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:50:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:50:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:50:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:50:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:50:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:50:26] Please supply a reference FASTA/GBK/EMBL file with --reference
3[06:51:40] This is snippy 4.6.0
Show full stderr[06:51:40] This is snippy 4.6.0 [06:51:40] Written by Torsten Seemann [06:51:40] Obtained from https://github.com/tseemann/snippy [06:51:40] Detected operating system: linux [06:51:40] Enabling bundled linux tools. [06:51:40] Found bwa - /usr/local/bin/bwa [06:51:40] Found bcftools - /usr/local/bin/bcftools [06:51:40] Found samtools - /usr/local/bin/samtools [06:51:40] Found java - /usr/local/bin/java [06:51:40] Found snpEff - /usr/local/bin/snpEff [06:51:40] Found samclip - /usr/local/bin/samclip [06:51:40] Found seqtk - /usr/local/bin/seqtk [06:51:40] Found parallel - /usr/local/bin/parallel [06:51:40] Found freebayes - /usr/local/bin/freebayes [06:51:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:51:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:51:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:51:40] Found vcfuniq - /usr/local/bin/vcfuniq [06:51:40] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:51:40] Found gzip - /bin/gzip [06:51:40] Found vt - /usr/local/bin/vt [06:51:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:51:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:51:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:51:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:51:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:51:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:51:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:51:41] Please supply a reference FASTA/GBK/EMBL file with --reference
3[06:52:10] This is snippy 4.6.0
Show full stderr[06:52:10] This is snippy 4.6.0 [06:52:10] Written by Torsten Seemann [06:52:10] Obtained from https://github.com/tseemann/snippy [06:52:10] Detected operating system: linux [06:52:10] Enabling bundled linux tools. [06:52:10] Found bwa - /usr/local/bin/bwa [06:52:10] Found bcftools - /usr/local/bin/bcftools [06:52:10] Found samtools - /usr/local/bin/samtools [06:52:10] Found java - /usr/local/bin/java [06:52:10] Found snpEff - /usr/local/bin/snpEff [06:52:10] Found samclip - /usr/local/bin/samclip [06:52:10] Found seqtk - /usr/local/bin/seqtk [06:52:10] Found parallel - /usr/local/bin/parallel [06:52:10] Found freebayes - /usr/local/bin/freebayes [06:52:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:52:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:52:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:52:10] Found vcfuniq - /usr/local/bin/vcfuniq [06:52:10] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:52:10] Found gzip - /bin/gzip [06:52:10] Found vt - /usr/local/bin/vt [06:52:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:52:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:52:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:52:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:52:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:52:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:52:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:52:11] Please supply a reference FASTA/GBK/EMBL file with --reference
3[06:50:38] This is snippy 4.6.0
Show full stderr[06:50:38] This is snippy 4.6.0 [06:50:38] Written by Torsten Seemann [06:50:38] Obtained from https://github.com/tseemann/snippy [06:50:38] Detected operating system: linux [06:50:38] Enabling bundled linux tools. [06:50:38] Found bwa - /usr/local/bin/bwa [06:50:38] Found bcftools - /usr/local/bin/bcftools [06:50:38] Found samtools - /usr/local/bin/samtools [06:50:38] Found java - /usr/local/bin/java [06:50:38] Found snpEff - /usr/local/bin/snpEff [06:50:38] Found samclip - /usr/local/bin/samclip [06:50:38] Found seqtk - /usr/local/bin/seqtk [06:50:38] Found parallel - /usr/local/bin/parallel [06:50:38] Found freebayes - /usr/local/bin/freebayes [06:50:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:50:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:50:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:50:38] Found vcfuniq - /usr/local/bin/vcfuniq [06:50:38] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:50:38] Found gzip - /bin/gzip [06:50:38] Found vt - /usr/local/bin/vt [06:50:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:50:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:50:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:50:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:50:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:50:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:50:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:50:39] Please supply a reference FASTA/GBK/EMBL file with --reference
3[06:51:55] This is snippy 4.6.0
Show full stderr[06:51:55] This is snippy 4.6.0 [06:51:55] Written by Torsten Seemann [06:51:55] Obtained from https://github.com/tseemann/snippy [06:51:55] Detected operating system: linux [06:51:55] Enabling bundled linux tools. [06:51:55] Found bwa - /usr/local/bin/bwa [06:51:55] Found bcftools - /usr/local/bin/bcftools [06:51:55] Found samtools - /usr/local/bin/samtools [06:51:55] Found java - /usr/local/bin/java [06:51:55] Found snpEff - /usr/local/bin/snpEff [06:51:55] Found samclip - /usr/local/bin/samclip [06:51:55] Found seqtk - /usr/local/bin/seqtk [06:51:55] Found parallel - /usr/local/bin/parallel [06:51:55] Found freebayes - /usr/local/bin/freebayes [06:51:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:51:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:51:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:51:55] Found vcfuniq - /usr/local/bin/vcfuniq [06:51:55] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:51:55] Found gzip - /bin/gzip [06:51:55] Found vt - /usr/local/bin/vt [06:51:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:51:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:51:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:51:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:51:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:51:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:51:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:51:56] Please supply a reference FASTA/GBK/EMBL file with --reference
3[06:54:28] This is snippy 4.6.0
Show full stderr[06:54:28] This is snippy 4.6.0 [06:54:28] Written by Torsten Seemann [06:54:28] Obtained from https://github.com/tseemann/snippy [06:54:28] Detected operating system: linux [06:54:28] Enabling bundled linux tools. [06:54:28] Found bwa - /usr/local/bin/bwa [06:54:28] Found bcftools - /usr/local/bin/bcftools [06:54:28] Found samtools - /usr/local/bin/samtools [06:54:28] Found java - /usr/local/bin/java [06:54:28] Found snpEff - /usr/local/bin/snpEff [06:54:28] Found samclip - /usr/local/bin/samclip [06:54:28] Found seqtk - /usr/local/bin/seqtk [06:54:28] Found parallel - /usr/local/bin/parallel [06:54:28] Found freebayes - /usr/local/bin/freebayes [06:54:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:54:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:54:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:54:28] Found vcfuniq - /usr/local/bin/vcfuniq [06:54:28] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:54:28] Found gzip - /bin/gzip [06:54:28] Found vt - /usr/local/bin/vt [06:54:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:54:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:54:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:54:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:54:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:54:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:54:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:54:29] Please supply a reference FASTA/GBK/EMBL file with --reference
3[06:51:28] This is snippy 4.6.0
Show full stderr[06:51:28] This is snippy 4.6.0 [06:51:28] Written by Torsten Seemann [06:51:28] Obtained from https://github.com/tseemann/snippy [06:51:28] Detected operating system: linux [06:51:28] Enabling bundled linux tools. [06:51:28] Found bwa - /usr/local/bin/bwa [06:51:28] Found bcftools - /usr/local/bin/bcftools [06:51:28] Found samtools - /usr/local/bin/samtools [06:51:28] Found java - /usr/local/bin/java [06:51:28] Found snpEff - /usr/local/bin/snpEff [06:51:28] Found samclip - /usr/local/bin/samclip [06:51:28] Found seqtk - /usr/local/bin/seqtk [06:51:28] Found parallel - /usr/local/bin/parallel [06:51:28] Found freebayes - /usr/local/bin/freebayes [06:51:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:51:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:51:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:51:28] Found vcfuniq - /usr/local/bin/vcfuniq [06:51:28] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:51:28] Found gzip - /bin/gzip [06:51:28] Found vt - /usr/local/bin/vt [06:51:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:51:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:51:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:51:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:51:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:51:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:51:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:51:29] Please supply a reference FASTA/GBK/EMBL file with --reference
3[06:54:43] This is snippy 4.6.0
Show full stderr[06:54:43] This is snippy 4.6.0 [06:54:43] Written by Torsten Seemann [06:54:43] Obtained from https://github.com/tseemann/snippy [06:54:43] Detected operating system: linux [06:54:43] Enabling bundled linux tools. [06:54:43] Found bwa - /usr/local/bin/bwa [06:54:43] Found bcftools - /usr/local/bin/bcftools [06:54:43] Found samtools - /usr/local/bin/samtools [06:54:43] Found java - /usr/local/bin/java [06:54:43] Found snpEff - /usr/local/bin/snpEff [06:54:43] Found samclip - /usr/local/bin/samclip [06:54:43] Found seqtk - /usr/local/bin/seqtk [06:54:43] Found parallel - /usr/local/bin/parallel [06:54:43] Found freebayes - /usr/local/bin/freebayes [06:54:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:54:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:54:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:54:43] Found vcfuniq - /usr/local/bin/vcfuniq [06:54:43] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:54:43] Found gzip - /bin/gzip [06:54:43] Found vt - /usr/local/bin/vt [06:54:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:54:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:54:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:54:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:54:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:54:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:54:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:54:44] Please supply a reference FASTA/GBK/EMBL file with --reference
3[06:54:55] This is snippy 4.6.0
Show full stderr[06:54:55] This is snippy 4.6.0 [06:54:55] Written by Torsten Seemann [06:54:55] Obtained from https://github.com/tseemann/snippy [06:54:55] Detected operating system: linux [06:54:55] Enabling bundled linux tools. [06:54:55] Found bwa - /usr/local/bin/bwa [06:54:55] Found bcftools - /usr/local/bin/bcftools [06:54:55] Found samtools - /usr/local/bin/samtools [06:54:55] Found java - /usr/local/bin/java [06:54:55] Found snpEff - /usr/local/bin/snpEff [06:54:55] Found samclip - /usr/local/bin/samclip [06:54:55] Found seqtk - /usr/local/bin/seqtk [06:54:55] Found parallel - /usr/local/bin/parallel [06:54:55] Found freebayes - /usr/local/bin/freebayes [06:54:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:54:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:54:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:54:55] Found vcfuniq - /usr/local/bin/vcfuniq [06:54:55] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:54:55] Found gzip - /bin/gzip [06:54:55] Found vt - /usr/local/bin/vt [06:54:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:54:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:54:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:54:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:54:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:54:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:54:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:54:56] Please supply a reference FASTA/GBK/EMBL file with --reference
3[06:56:27] This is snippy 4.6.0
Show full stderr[06:56:27] This is snippy 4.6.0 [06:56:27] Written by Torsten Seemann [06:56:27] Obtained from https://github.com/tseemann/snippy [06:56:27] Detected operating system: linux [06:56:27] Enabling bundled linux tools. [06:56:27] Found bwa - /usr/local/bin/bwa [06:56:27] Found bcftools - /usr/local/bin/bcftools [06:56:27] Found samtools - /usr/local/bin/samtools [06:56:27] Found java - /usr/local/bin/java [06:56:27] Found snpEff - /usr/local/bin/snpEff [06:56:27] Found samclip - /usr/local/bin/samclip [06:56:27] Found seqtk - /usr/local/bin/seqtk [06:56:27] Found parallel - /usr/local/bin/parallel [06:56:27] Found freebayes - /usr/local/bin/freebayes [06:56:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:56:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:56:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:56:27] Found vcfuniq - /usr/local/bin/vcfuniq [06:56:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:56:27] Found gzip - /bin/gzip [06:56:27] Found vt - /usr/local/bin/vt [06:56:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:56:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:56:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:56:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:56:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:56:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:56:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:56:28] Please supply a reference FASTA/GBK/EMBL file with --reference
3[06:56:41] This is snippy 4.6.0
Show full stderr[06:56:41] This is snippy 4.6.0 [06:56:41] Written by Torsten Seemann [06:56:41] Obtained from https://github.com/tseemann/snippy [06:56:41] Detected operating system: linux [06:56:41] Enabling bundled linux tools. [06:56:41] Found bwa - /usr/local/bin/bwa [06:56:41] Found bcftools - /usr/local/bin/bcftools [06:56:41] Found samtools - /usr/local/bin/samtools [06:56:41] Found java - /usr/local/bin/java [06:56:41] Found snpEff - /usr/local/bin/snpEff [06:56:41] Found samclip - /usr/local/bin/samclip [06:56:41] Found seqtk - /usr/local/bin/seqtk [06:56:41] Found parallel - /usr/local/bin/parallel [06:56:41] Found freebayes - /usr/local/bin/freebayes [06:56:41] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:56:41] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:56:41] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:56:41] Found vcfuniq - /usr/local/bin/vcfuniq [06:56:41] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:56:41] Found gzip - /bin/gzip [06:56:41] Found vt - /usr/local/bin/vt [06:56:41] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:56:41] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:56:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:56:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:56:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:56:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:56:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:56:42] Please supply a reference FASTA/GBK/EMBL file with --reference
3[06:57:10] This is snippy 4.6.0
Show full stderr[06:57:10] This is snippy 4.6.0 [06:57:10] Written by Torsten Seemann [06:57:10] Obtained from https://github.com/tseemann/snippy [06:57:10] Detected operating system: linux [06:57:10] Enabling bundled linux tools. [06:57:10] Found bwa - /usr/local/bin/bwa [06:57:10] Found bcftools - /usr/local/bin/bcftools [06:57:10] Found samtools - /usr/local/bin/samtools [06:57:10] Found java - /usr/local/bin/java [06:57:10] Found snpEff - /usr/local/bin/snpEff [06:57:10] Found samclip - /usr/local/bin/samclip [06:57:10] Found seqtk - /usr/local/bin/seqtk [06:57:10] Found parallel - /usr/local/bin/parallel [06:57:10] Found freebayes - /usr/local/bin/freebayes [06:57:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:57:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:57:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:57:10] Found vcfuniq - /usr/local/bin/vcfuniq [06:57:10] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:57:10] Found gzip - /bin/gzip [06:57:10] Found vt - /usr/local/bin/vt [06:57:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:57:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:57:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:57:11] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:57:11] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:57:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:57:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:57:11] Please supply a reference FASTA/GBK/EMBL file with --reference
3[06:55:10] This is snippy 4.6.0
Show full stderr[06:55:10] This is snippy 4.6.0 [06:55:10] Written by Torsten Seemann [06:55:10] Obtained from https://github.com/tseemann/snippy [06:55:10] Detected operating system: linux [06:55:10] Enabling bundled linux tools. [06:55:10] Found bwa - /usr/local/bin/bwa [06:55:10] Found bcftools - /usr/local/bin/bcftools [06:55:10] Found samtools - /usr/local/bin/samtools [06:55:10] Found java - /usr/local/bin/java [06:55:10] Found snpEff - /usr/local/bin/snpEff [06:55:10] Found samclip - /usr/local/bin/samclip [06:55:10] Found seqtk - /usr/local/bin/seqtk [06:55:10] Found parallel - /usr/local/bin/parallel [06:55:10] Found freebayes - /usr/local/bin/freebayes [06:55:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:55:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:55:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:55:10] Found vcfuniq - /usr/local/bin/vcfuniq [06:55:10] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:55:10] Found gzip - /bin/gzip [06:55:10] Found vt - /usr/local/bin/vt [06:55:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:55:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:55:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:55:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:55:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:55:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:55:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:55:11] Please supply a reference FASTA/GBK/EMBL file with --reference
3[06:59:27] This is snippy 4.6.0
Show full stderr[06:59:27] This is snippy 4.6.0 [06:59:27] Written by Torsten Seemann [06:59:27] Obtained from https://github.com/tseemann/snippy [06:59:27] Detected operating system: linux [06:59:27] Enabling bundled linux tools. [06:59:27] Found bwa - /usr/local/bin/bwa [06:59:27] Found bcftools - /usr/local/bin/bcftools [06:59:27] Found samtools - /usr/local/bin/samtools [06:59:28] Found java - /usr/local/bin/java [06:59:28] Found snpEff - /usr/local/bin/snpEff [06:59:28] Found samclip - /usr/local/bin/samclip [06:59:28] Found seqtk - /usr/local/bin/seqtk [06:59:28] Found parallel - /usr/local/bin/parallel [06:59:28] Found freebayes - /usr/local/bin/freebayes [06:59:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:59:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:59:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:59:28] Found vcfuniq - /usr/local/bin/vcfuniq [06:59:28] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:59:28] Found gzip - /bin/gzip [06:59:28] Found vt - /usr/local/bin/vt [06:59:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:59:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:59:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:59:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:59:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:59:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:59:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:59:28] Please supply a reference FASTA/GBK/EMBL file with --reference
3[07:01:36] This is snippy 4.6.0
Show full stderr[07:01:36] This is snippy 4.6.0 [07:01:36] Written by Torsten Seemann [07:01:36] Obtained from https://github.com/tseemann/snippy [07:01:36] Detected operating system: linux [07:01:36] Enabling bundled linux tools. [07:01:36] Found bwa - /usr/local/bin/bwa [07:01:36] Found bcftools - /usr/local/bin/bcftools [07:01:36] Found samtools - /usr/local/bin/samtools [07:01:36] Found java - /usr/local/bin/java [07:01:36] Found snpEff - /usr/local/bin/snpEff [07:01:36] Found samclip - /usr/local/bin/samclip [07:01:36] Found seqtk - /usr/local/bin/seqtk [07:01:36] Found parallel - /usr/local/bin/parallel [07:01:36] Found freebayes - /usr/local/bin/freebayes [07:01:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:01:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:01:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:01:36] Found vcfuniq - /usr/local/bin/vcfuniq [07:01:36] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:01:36] Found gzip - /bin/gzip [07:01:36] Found vt - /usr/local/bin/vt [07:01:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:01:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:01:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:01:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:01:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:01:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:01:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:01:37] Please supply a reference FASTA/GBK/EMBL file with --reference
3[07:01:50] This is snippy 4.6.0
Show full stderr[07:01:50] This is snippy 4.6.0 [07:01:50] Written by Torsten Seemann [07:01:50] Obtained from https://github.com/tseemann/snippy [07:01:50] Detected operating system: linux [07:01:50] Enabling bundled linux tools. [07:01:50] Found bwa - /usr/local/bin/bwa [07:01:50] Found bcftools - /usr/local/bin/bcftools [07:01:50] Found samtools - /usr/local/bin/samtools [07:01:50] Found java - /usr/local/bin/java [07:01:50] Found snpEff - /usr/local/bin/snpEff [07:01:50] Found samclip - /usr/local/bin/samclip [07:01:50] Found seqtk - /usr/local/bin/seqtk [07:01:50] Found parallel - /usr/local/bin/parallel [07:01:50] Found freebayes - /usr/local/bin/freebayes [07:01:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:01:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:01:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:01:50] Found vcfuniq - /usr/local/bin/vcfuniq [07:01:50] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:01:50] Found gzip - /bin/gzip [07:01:50] Found vt - /usr/local/bin/vt [07:01:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:01:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:01:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:01:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:01:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:01:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:01:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:01:51] Please supply a reference FASTA/GBK/EMBL file with --reference
3[06:57:35] This is snippy 4.6.0
Show full stderr[06:57:35] This is snippy 4.6.0 [06:57:35] Written by Torsten Seemann [06:57:35] Obtained from https://github.com/tseemann/snippy [06:57:35] Detected operating system: linux [06:57:35] Enabling bundled linux tools. [06:57:35] Found bwa - /usr/local/bin/bwa [06:57:35] Found bcftools - /usr/local/bin/bcftools [06:57:35] Found samtools - /usr/local/bin/samtools [06:57:35] Found java - /usr/local/bin/java [06:57:35] Found snpEff - /usr/local/bin/snpEff [06:57:35] Found samclip - /usr/local/bin/samclip [06:57:35] Found seqtk - /usr/local/bin/seqtk [06:57:35] Found parallel - /usr/local/bin/parallel [06:57:35] Found freebayes - /usr/local/bin/freebayes [06:57:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:57:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:57:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:57:35] Found vcfuniq - /usr/local/bin/vcfuniq [06:57:35] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:57:35] Found gzip - /bin/gzip [06:57:35] Found vt - /usr/local/bin/vt [06:57:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:57:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:57:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:57:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:57:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:57:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:57:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:57:36] Please supply a reference FASTA/GBK/EMBL file with --reference
3[06:57:50] This is snippy 4.6.0
Show full stderr[06:57:50] This is snippy 4.6.0 [06:57:50] Written by Torsten Seemann [06:57:50] Obtained from https://github.com/tseemann/snippy [06:57:50] Detected operating system: linux [06:57:50] Enabling bundled linux tools. [06:57:50] Found bwa - /usr/local/bin/bwa [06:57:50] Found bcftools - /usr/local/bin/bcftools [06:57:50] Found samtools - /usr/local/bin/samtools [06:57:50] Found java - /usr/local/bin/java [06:57:50] Found snpEff - /usr/local/bin/snpEff [06:57:50] Found samclip - /usr/local/bin/samclip [06:57:50] Found seqtk - /usr/local/bin/seqtk [06:57:50] Found parallel - /usr/local/bin/parallel [06:57:50] Found freebayes - /usr/local/bin/freebayes [06:57:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:57:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:57:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:57:50] Found vcfuniq - /usr/local/bin/vcfuniq [06:57:50] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:57:50] Found gzip - /bin/gzip [06:57:50] Found vt - /usr/local/bin/vt [06:57:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:57:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:57:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:57:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:57:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:57:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:57:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:57:51] Please supply a reference FASTA/GBK/EMBL file with --reference
3[06:56:55] This is snippy 4.6.0
Show full stderr[06:56:55] This is snippy 4.6.0 [06:56:55] Written by Torsten Seemann [06:56:55] Obtained from https://github.com/tseemann/snippy [06:56:55] Detected operating system: linux [06:56:55] Enabling bundled linux tools. [06:56:55] Found bwa - /usr/local/bin/bwa [06:56:55] Found bcftools - /usr/local/bin/bcftools [06:56:55] Found samtools - /usr/local/bin/samtools [06:56:55] Found java - /usr/local/bin/java [06:56:55] Found snpEff - /usr/local/bin/snpEff [06:56:55] Found samclip - /usr/local/bin/samclip [06:56:55] Found seqtk - /usr/local/bin/seqtk [06:56:55] Found parallel - /usr/local/bin/parallel [06:56:55] Found freebayes - /usr/local/bin/freebayes [06:56:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:56:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:56:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:56:55] Found vcfuniq - /usr/local/bin/vcfuniq [06:56:55] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:56:55] Found gzip - /bin/gzip [06:56:55] Found vt - /usr/local/bin/vt [06:56:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:56:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:56:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:56:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:56:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:56:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:56:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:56:56] Please supply a reference FASTA/GBK/EMBL file with --reference
3[07:02:04] This is snippy 4.6.0
Show full stderr[07:02:04] This is snippy 4.6.0 [07:02:04] Written by Torsten Seemann [07:02:04] Obtained from https://github.com/tseemann/snippy [07:02:04] Detected operating system: linux [07:02:04] Enabling bundled linux tools. [07:02:04] Found bwa - /usr/local/bin/bwa [07:02:04] Found bcftools - /usr/local/bin/bcftools [07:02:04] Found samtools - /usr/local/bin/samtools [07:02:04] Found java - /usr/local/bin/java [07:02:04] Found snpEff - /usr/local/bin/snpEff [07:02:04] Found samclip - /usr/local/bin/samclip [07:02:04] Found seqtk - /usr/local/bin/seqtk [07:02:04] Found parallel - /usr/local/bin/parallel [07:02:04] Found freebayes - /usr/local/bin/freebayes [07:02:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:02:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:02:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:02:04] Found vcfuniq - /usr/local/bin/vcfuniq [07:02:04] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:02:04] Found gzip - /bin/gzip [07:02:04] Found vt - /usr/local/bin/vt [07:02:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:02:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:02:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:02:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:02:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:02:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:02:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:02:05] Please supply a reference FASTA/GBK/EMBL file with --reference
3[07:02:19] This is snippy 4.6.0
Show full stderr[07:02:19] This is snippy 4.6.0 [07:02:19] Written by Torsten Seemann [07:02:19] Obtained from https://github.com/tseemann/snippy [07:02:19] Detected operating system: linux [07:02:19] Enabling bundled linux tools. [07:02:19] Found bwa - /usr/local/bin/bwa [07:02:19] Found bcftools - /usr/local/bin/bcftools [07:02:19] Found samtools - /usr/local/bin/samtools [07:02:19] Found java - /usr/local/bin/java [07:02:19] Found snpEff - /usr/local/bin/snpEff [07:02:19] Found samclip - /usr/local/bin/samclip [07:02:19] Found seqtk - /usr/local/bin/seqtk [07:02:19] Found parallel - /usr/local/bin/parallel [07:02:19] Found freebayes - /usr/local/bin/freebayes [07:02:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:02:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:02:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:02:19] Found vcfuniq - /usr/local/bin/vcfuniq [07:02:19] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:02:19] Found gzip - /bin/gzip [07:02:19] Found vt - /usr/local/bin/vt [07:02:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:02:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:02:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:02:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:02:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:02:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:02:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:02:20] Please supply a reference FASTA/GBK/EMBL file with --reference
3[07:05:20] This is snippy 4.6.0
Show full stderr[07:05:20] This is snippy 4.6.0 [07:05:20] Written by Torsten Seemann [07:05:20] Obtained from https://github.com/tseemann/snippy [07:05:20] Detected operating system: linux [07:05:20] Enabling bundled linux tools. [07:05:20] Found bwa - /usr/local/bin/bwa [07:05:20] Found bcftools - /usr/local/bin/bcftools [07:05:20] Found samtools - /usr/local/bin/samtools [07:05:20] Found java - /usr/local/bin/java [07:05:20] Found snpEff - /usr/local/bin/snpEff [07:05:20] Found samclip - /usr/local/bin/samclip [07:05:20] Found seqtk - /usr/local/bin/seqtk [07:05:20] Found parallel - /usr/local/bin/parallel [07:05:20] Found freebayes - /usr/local/bin/freebayes [07:05:20] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:05:20] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:05:20] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:05:20] Found vcfuniq - /usr/local/bin/vcfuniq [07:05:20] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:05:20] Found gzip - /bin/gzip [07:05:20] Found vt - /usr/local/bin/vt [07:05:20] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:05:20] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:05:20] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:05:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:05:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:05:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:05:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:05:21] Please supply a reference FASTA/GBK/EMBL file with --reference
3[07:02:31] This is snippy 4.6.0
Show full stderr[07:02:31] This is snippy 4.6.0 [07:02:31] Written by Torsten Seemann [07:02:31] Obtained from https://github.com/tseemann/snippy [07:02:31] Detected operating system: linux [07:02:31] Enabling bundled linux tools. [07:02:31] Found bwa - /usr/local/bin/bwa [07:02:31] Found bcftools - /usr/local/bin/bcftools [07:02:31] Found samtools - /usr/local/bin/samtools [07:02:31] Found java - /usr/local/bin/java [07:02:31] Found snpEff - /usr/local/bin/snpEff [07:02:31] Found samclip - /usr/local/bin/samclip [07:02:31] Found seqtk - /usr/local/bin/seqtk [07:02:31] Found parallel - /usr/local/bin/parallel [07:02:31] Found freebayes - /usr/local/bin/freebayes [07:02:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:02:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:02:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:02:31] Found vcfuniq - /usr/local/bin/vcfuniq [07:02:31] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:02:31] Found gzip - /bin/gzip [07:02:31] Found vt - /usr/local/bin/vt [07:02:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:02:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:02:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:02:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:02:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:02:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:02:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:02:32] Please supply a reference FASTA/GBK/EMBL file with --reference
3[07:15:07] This is snippy 4.6.0
Show full stderr[07:15:07] This is snippy 4.6.0 [07:15:07] Written by Torsten Seemann [07:15:07] Obtained from https://github.com/tseemann/snippy [07:15:07] Detected operating system: linux [07:15:07] Enabling bundled linux tools. [07:15:07] Found bwa - /usr/local/bin/bwa [07:15:07] Found bcftools - /usr/local/bin/bcftools [07:15:07] Found samtools - /usr/local/bin/samtools [07:15:07] Found java - /usr/local/bin/java [07:15:07] Found snpEff - /usr/local/bin/snpEff [07:15:07] Found samclip - /usr/local/bin/samclip [07:15:07] Found seqtk - /usr/local/bin/seqtk [07:15:07] Found parallel - /usr/local/bin/parallel [07:15:07] Found freebayes - /usr/local/bin/freebayes [07:15:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:15:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:15:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:15:07] Found vcfuniq - /usr/local/bin/vcfuniq [07:15:07] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:15:07] Found gzip - /bin/gzip [07:15:07] Found vt - /usr/local/bin/vt [07:15:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:15:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:15:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:15:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:15:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:15:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:15:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:15:08] Please supply a reference FASTA/GBK/EMBL file with --reference
3[07:10:57] This is snippy 4.6.0
Show full stderr[07:10:57] This is snippy 4.6.0 [07:10:57] Written by Torsten Seemann [07:10:57] Obtained from https://github.com/tseemann/snippy [07:10:57] Detected operating system: linux [07:10:57] Enabling bundled linux tools. [07:10:57] Found bwa - /usr/local/bin/bwa [07:10:57] Found bcftools - /usr/local/bin/bcftools [07:10:57] Found samtools - /usr/local/bin/samtools [07:10:57] Found java - /usr/local/bin/java [07:10:57] Found snpEff - /usr/local/bin/snpEff [07:10:57] Found samclip - /usr/local/bin/samclip [07:10:57] Found seqtk - /usr/local/bin/seqtk [07:10:57] Found parallel - /usr/local/bin/parallel [07:10:57] Found freebayes - /usr/local/bin/freebayes [07:10:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:10:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:10:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:10:57] Found vcfuniq - /usr/local/bin/vcfuniq [07:10:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:10:57] Found gzip - /bin/gzip [07:10:57] Found vt - /usr/local/bin/vt [07:10:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:10:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:10:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:10:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:10:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:10:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:10:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:10:58] Please supply a reference FASTA/GBK/EMBL file with --reference
3[07:11:10] This is snippy 4.6.0
Show full stderr[07:11:10] This is snippy 4.6.0 [07:11:10] Written by Torsten Seemann [07:11:10] Obtained from https://github.com/tseemann/snippy [07:11:10] Detected operating system: linux [07:11:10] Enabling bundled linux tools. [07:11:10] Found bwa - /usr/local/bin/bwa [07:11:10] Found bcftools - /usr/local/bin/bcftools [07:11:10] Found samtools - /usr/local/bin/samtools [07:11:10] Found java - /usr/local/bin/java [07:11:10] Found snpEff - /usr/local/bin/snpEff [07:11:10] Found samclip - /usr/local/bin/samclip [07:11:10] Found seqtk - /usr/local/bin/seqtk [07:11:10] Found parallel - /usr/local/bin/parallel [07:11:10] Found freebayes - /usr/local/bin/freebayes [07:11:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:11:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:11:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:11:10] Found vcfuniq - /usr/local/bin/vcfuniq [07:11:10] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:11:10] Found gzip - /bin/gzip [07:11:10] Found vt - /usr/local/bin/vt [07:11:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:11:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:11:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:11:11] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:11:11] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:11:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:11:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:11:11] Please supply a reference FASTA/GBK/EMBL file with --reference
3[07:11:23] This is snippy 4.6.0
Show full stderr[07:11:23] This is snippy 4.6.0 [07:11:23] Written by Torsten Seemann [07:11:23] Obtained from https://github.com/tseemann/snippy [07:11:23] Detected operating system: linux [07:11:23] Enabling bundled linux tools. [07:11:23] Found bwa - /usr/local/bin/bwa [07:11:23] Found bcftools - /usr/local/bin/bcftools [07:11:23] Found samtools - /usr/local/bin/samtools [07:11:23] Found java - /usr/local/bin/java [07:11:23] Found snpEff - /usr/local/bin/snpEff [07:11:23] Found samclip - /usr/local/bin/samclip [07:11:23] Found seqtk - /usr/local/bin/seqtk [07:11:23] Found parallel - /usr/local/bin/parallel [07:11:23] Found freebayes - /usr/local/bin/freebayes [07:11:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:11:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:11:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:11:23] Found vcfuniq - /usr/local/bin/vcfuniq [07:11:23] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:11:23] Found gzip - /bin/gzip [07:11:23] Found vt - /usr/local/bin/vt [07:11:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:11:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:11:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:11:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:11:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:11:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:11:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:11:24] Please supply a reference FASTA/GBK/EMBL file with --reference
3[07:14:54] This is snippy 4.6.0
Show full stderr[07:14:54] This is snippy 4.6.0 [07:14:54] Written by Torsten Seemann [07:14:54] Obtained from https://github.com/tseemann/snippy [07:14:54] Detected operating system: linux [07:14:54] Enabling bundled linux tools. [07:14:54] Found bwa - /usr/local/bin/bwa [07:14:54] Found bcftools - /usr/local/bin/bcftools [07:14:54] Found samtools - /usr/local/bin/samtools [07:14:54] Found java - /usr/local/bin/java [07:14:54] Found snpEff - /usr/local/bin/snpEff [07:14:54] Found samclip - /usr/local/bin/samclip [07:14:54] Found seqtk - /usr/local/bin/seqtk [07:14:54] Found parallel - /usr/local/bin/parallel [07:14:54] Found freebayes - /usr/local/bin/freebayes [07:14:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:14:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:14:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:14:54] Found vcfuniq - /usr/local/bin/vcfuniq [07:14:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:14:54] Found gzip - /bin/gzip [07:14:54] Found vt - /usr/local/bin/vt [07:14:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:14:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:14:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:14:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:14:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:14:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:14:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:14:54] Please supply a reference FASTA/GBK/EMBL file with --reference
3[07:14:28] This is snippy 4.6.0
Show full stderr[07:14:28] This is snippy 4.6.0 [07:14:28] Written by Torsten Seemann [07:14:28] Obtained from https://github.com/tseemann/snippy [07:14:28] Detected operating system: linux [07:14:28] Enabling bundled linux tools. [07:14:28] Found bwa - /usr/local/bin/bwa [07:14:28] Found bcftools - /usr/local/bin/bcftools [07:14:28] Found samtools - /usr/local/bin/samtools [07:14:28] Found java - /usr/local/bin/java [07:14:28] Found snpEff - /usr/local/bin/snpEff [07:14:28] Found samclip - /usr/local/bin/samclip [07:14:28] Found seqtk - /usr/local/bin/seqtk [07:14:28] Found parallel - /usr/local/bin/parallel [07:14:28] Found freebayes - /usr/local/bin/freebayes [07:14:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:14:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:14:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:14:28] Found vcfuniq - /usr/local/bin/vcfuniq [07:14:28] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:14:28] Found gzip - /bin/gzip [07:14:28] Found vt - /usr/local/bin/vt [07:14:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:14:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:14:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:14:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:14:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:14:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:14:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:14:28] Please supply a reference FASTA/GBK/EMBL file with --reference
3[07:29:34] This is snippy 4.6.0
Show full stderr[07:29:34] This is snippy 4.6.0 [07:29:34] Written by Torsten Seemann [07:29:34] Obtained from https://github.com/tseemann/snippy [07:29:34] Detected operating system: linux [07:29:34] Enabling bundled linux tools. [07:29:34] Found bwa - /usr/local/bin/bwa [07:29:34] Found bcftools - /usr/local/bin/bcftools [07:29:34] Found samtools - /usr/local/bin/samtools [07:29:34] Found java - /usr/local/bin/java [07:29:34] Found snpEff - /usr/local/bin/snpEff [07:29:34] Found samclip - /usr/local/bin/samclip [07:29:34] Found seqtk - /usr/local/bin/seqtk [07:29:34] Found parallel - /usr/local/bin/parallel [07:29:34] Found freebayes - /usr/local/bin/freebayes [07:29:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:29:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:29:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:29:34] Found vcfuniq - /usr/local/bin/vcfuniq [07:29:34] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:29:34] Found gzip - /bin/gzip [07:29:34] Found vt - /usr/local/bin/vt [07:29:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:29:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:29:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:29:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:29:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:29:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:29:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:29:35] Please supply a reference FASTA/GBK/EMBL file with --reference
3[07:31:21] This is snippy 4.6.0
Show full stderr[07:31:21] This is snippy 4.6.0 [07:31:21] Written by Torsten Seemann [07:31:21] Obtained from https://github.com/tseemann/snippy [07:31:21] Detected operating system: linux [07:31:21] Enabling bundled linux tools. [07:31:21] Found bwa - /usr/local/bin/bwa [07:31:21] Found bcftools - /usr/local/bin/bcftools [07:31:21] Found samtools - /usr/local/bin/samtools [07:31:21] Found java - /usr/local/bin/java [07:31:21] Found snpEff - /usr/local/bin/snpEff [07:31:21] Found samclip - /usr/local/bin/samclip [07:31:21] Found seqtk - /usr/local/bin/seqtk [07:31:21] Found parallel - /usr/local/bin/parallel [07:31:21] Found freebayes - /usr/local/bin/freebayes [07:31:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:31:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:31:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:31:21] Found vcfuniq - /usr/local/bin/vcfuniq [07:31:21] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:31:21] Found gzip - /bin/gzip [07:31:21] Found vt - /usr/local/bin/vt [07:31:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:31:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:31:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:31:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:31:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:31:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:31:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:31:22] Please supply a reference FASTA/GBK/EMBL file with --reference
3[07:32:14] This is snippy 4.6.0
Show full stderr[07:32:14] This is snippy 4.6.0 [07:32:14] Written by Torsten Seemann [07:32:14] Obtained from https://github.com/tseemann/snippy [07:32:14] Detected operating system: linux [07:32:14] Enabling bundled linux tools. [07:32:14] Found bwa - /usr/local/bin/bwa [07:32:14] Found bcftools - /usr/local/bin/bcftools [07:32:14] Found samtools - /usr/local/bin/samtools [07:32:14] Found java - /usr/local/bin/java [07:32:14] Found snpEff - /usr/local/bin/snpEff [07:32:14] Found samclip - /usr/local/bin/samclip [07:32:14] Found seqtk - /usr/local/bin/seqtk [07:32:14] Found parallel - /usr/local/bin/parallel [07:32:14] Found freebayes - /usr/local/bin/freebayes [07:32:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:32:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:32:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:32:14] Found vcfuniq - /usr/local/bin/vcfuniq [07:32:14] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:32:14] Found gzip - /bin/gzip [07:32:14] Found vt - /usr/local/bin/vt [07:32:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:32:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:32:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:32:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:32:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:32:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:32:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:32:15] Please supply a reference FASTA/GBK/EMBL file with --reference
3[07:30:01] This is snippy 4.6.0
Show full stderr[07:30:01] This is snippy 4.6.0 [07:30:01] Written by Torsten Seemann [07:30:01] Obtained from https://github.com/tseemann/snippy [07:30:01] Detected operating system: linux [07:30:01] Enabling bundled linux tools. [07:30:01] Found bwa - /usr/local/bin/bwa [07:30:01] Found bcftools - /usr/local/bin/bcftools [07:30:01] Found samtools - /usr/local/bin/samtools [07:30:01] Found java - /usr/local/bin/java [07:30:01] Found snpEff - /usr/local/bin/snpEff [07:30:01] Found samclip - /usr/local/bin/samclip [07:30:01] Found seqtk - /usr/local/bin/seqtk [07:30:01] Found parallel - /usr/local/bin/parallel [07:30:01] Found freebayes - /usr/local/bin/freebayes [07:30:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:30:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:30:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:30:01] Found vcfuniq - /usr/local/bin/vcfuniq [07:30:01] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:30:01] Found gzip - /bin/gzip [07:30:01] Found vt - /usr/local/bin/vt [07:30:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:30:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:30:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:30:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:30:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:30:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:30:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:30:02] Please supply a reference FASTA/GBK/EMBL file with --reference
3[07:32:00] This is snippy 4.6.0
Show full stderr[07:32:00] This is snippy 4.6.0 [07:32:00] Written by Torsten Seemann [07:32:00] Obtained from https://github.com/tseemann/snippy [07:32:00] Detected operating system: linux [07:32:00] Enabling bundled linux tools. [07:32:00] Found bwa - /usr/local/bin/bwa [07:32:00] Found bcftools - /usr/local/bin/bcftools [07:32:00] Found samtools - /usr/local/bin/samtools [07:32:00] Found java - /usr/local/bin/java [07:32:00] Found snpEff - /usr/local/bin/snpEff [07:32:00] Found samclip - /usr/local/bin/samclip [07:32:00] Found seqtk - /usr/local/bin/seqtk [07:32:00] Found parallel - /usr/local/bin/parallel [07:32:00] Found freebayes - /usr/local/bin/freebayes [07:32:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:32:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:32:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:32:00] Found vcfuniq - /usr/local/bin/vcfuniq [07:32:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:32:00] Found gzip - /bin/gzip [07:32:00] Found vt - /usr/local/bin/vt [07:32:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:32:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:32:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:32:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:32:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:32:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:32:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:32:01] Please supply a reference FASTA/GBK/EMBL file with --reference
3[07:32:27] This is snippy 4.6.0
Show full stderr[07:32:27] This is snippy 4.6.0 [07:32:27] Written by Torsten Seemann [07:32:27] Obtained from https://github.com/tseemann/snippy [07:32:27] Detected operating system: linux [07:32:27] Enabling bundled linux tools. [07:32:27] Found bwa - /usr/local/bin/bwa [07:32:27] Found bcftools - /usr/local/bin/bcftools [07:32:27] Found samtools - /usr/local/bin/samtools [07:32:27] Found java - /usr/local/bin/java [07:32:27] Found snpEff - /usr/local/bin/snpEff [07:32:27] Found samclip - /usr/local/bin/samclip [07:32:27] Found seqtk - /usr/local/bin/seqtk [07:32:27] Found parallel - /usr/local/bin/parallel [07:32:27] Found freebayes - /usr/local/bin/freebayes [07:32:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:32:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:32:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:32:27] Found vcfuniq - /usr/local/bin/vcfuniq [07:32:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:32:27] Found gzip - /bin/gzip [07:32:27] Found vt - /usr/local/bin/vt [07:32:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:32:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:32:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:32:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:32:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:32:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:32:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:32:28] Please supply a reference FASTA/GBK/EMBL file with --reference
3[07:33:07] This is snippy 4.6.0
Show full stderr[07:33:07] This is snippy 4.6.0 [07:33:07] Written by Torsten Seemann [07:33:07] Obtained from https://github.com/tseemann/snippy [07:33:07] Detected operating system: linux [07:33:07] Enabling bundled linux tools. [07:33:07] Found bwa - /usr/local/bin/bwa [07:33:07] Found bcftools - /usr/local/bin/bcftools [07:33:07] Found samtools - /usr/local/bin/samtools [07:33:07] Found java - /usr/local/bin/java [07:33:07] Found snpEff - /usr/local/bin/snpEff [07:33:07] Found samclip - /usr/local/bin/samclip [07:33:07] Found seqtk - /usr/local/bin/seqtk [07:33:07] Found parallel - /usr/local/bin/parallel [07:33:07] Found freebayes - /usr/local/bin/freebayes [07:33:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:33:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:33:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:33:07] Found vcfuniq - /usr/local/bin/vcfuniq [07:33:07] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:33:07] Found gzip - /bin/gzip [07:33:07] Found vt - /usr/local/bin/vt [07:33:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:33:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:33:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:33:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:33:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:33:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:33:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:33:08] Please supply a reference FASTA/GBK/EMBL file with --reference
3[07:33:20] This is snippy 4.6.0
Show full stderr[07:33:20] This is snippy 4.6.0 [07:33:20] Written by Torsten Seemann [07:33:20] Obtained from https://github.com/tseemann/snippy [07:33:20] Detected operating system: linux [07:33:20] Enabling bundled linux tools. [07:33:20] Found bwa - /usr/local/bin/bwa [07:33:20] Found bcftools - /usr/local/bin/bcftools [07:33:20] Found samtools - /usr/local/bin/samtools [07:33:20] Found java - /usr/local/bin/java [07:33:20] Found snpEff - /usr/local/bin/snpEff [07:33:20] Found samclip - /usr/local/bin/samclip [07:33:20] Found seqtk - /usr/local/bin/seqtk [07:33:20] Found parallel - /usr/local/bin/parallel [07:33:20] Found freebayes - /usr/local/bin/freebayes [07:33:20] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:33:20] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:33:20] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:33:20] Found vcfuniq - /usr/local/bin/vcfuniq [07:33:20] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:33:20] Found gzip - /bin/gzip [07:33:20] Found vt - /usr/local/bin/vt [07:33:20] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:33:20] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:33:20] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:33:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:33:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:33:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:33:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:33:21] Please supply a reference FASTA/GBK/EMBL file with --reference
3[07:33:44] This is snippy 4.6.0
Show full stderr[07:33:44] This is snippy 4.6.0 [07:33:44] Written by Torsten Seemann [07:33:44] Obtained from https://github.com/tseemann/snippy [07:33:44] Detected operating system: linux [07:33:44] Enabling bundled linux tools. [07:33:44] Found bwa - /usr/local/bin/bwa [07:33:44] Found bcftools - /usr/local/bin/bcftools [07:33:44] Found samtools - /usr/local/bin/samtools [07:33:44] Found java - /usr/local/bin/java [07:33:44] Found snpEff - /usr/local/bin/snpEff [07:33:44] Found samclip - /usr/local/bin/samclip [07:33:44] Found seqtk - /usr/local/bin/seqtk [07:33:44] Found parallel - /usr/local/bin/parallel [07:33:44] Found freebayes - /usr/local/bin/freebayes [07:33:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:33:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:33:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:33:44] Found vcfuniq - /usr/local/bin/vcfuniq [07:33:44] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:33:44] Found gzip - /bin/gzip [07:33:44] Found vt - /usr/local/bin/vt [07:33:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:33:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:33:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:33:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:33:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:33:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:33:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:33:45] Please supply a reference FASTA/GBK/EMBL file with --reference
3[07:34:25] This is snippy 4.6.0
Show full stderr[07:34:25] This is snippy 4.6.0 [07:34:25] Written by Torsten Seemann [07:34:25] Obtained from https://github.com/tseemann/snippy [07:34:25] Detected operating system: linux [07:34:25] Enabling bundled linux tools. [07:34:25] Found bwa - /usr/local/bin/bwa [07:34:25] Found bcftools - /usr/local/bin/bcftools [07:34:25] Found samtools - /usr/local/bin/samtools [07:34:25] Found java - /usr/local/bin/java [07:34:25] Found snpEff - /usr/local/bin/snpEff [07:34:25] Found samclip - /usr/local/bin/samclip [07:34:25] Found seqtk - /usr/local/bin/seqtk [07:34:25] Found parallel - /usr/local/bin/parallel [07:34:25] Found freebayes - /usr/local/bin/freebayes [07:34:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:34:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:34:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:34:25] Found vcfuniq - /usr/local/bin/vcfuniq [07:34:25] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:34:25] Found gzip - /bin/gzip [07:34:25] Found vt - /usr/local/bin/vt [07:34:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:34:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:34:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:34:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:34:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:34:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:34:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:34:26] Please supply a reference FASTA/GBK/EMBL file with --reference
3[07:34:52] This is snippy 4.6.0
Show full stderr[07:34:52] This is snippy 4.6.0 [07:34:52] Written by Torsten Seemann [07:34:52] Obtained from https://github.com/tseemann/snippy [07:34:52] Detected operating system: linux [07:34:52] Enabling bundled linux tools. [07:34:52] Found bwa - /usr/local/bin/bwa [07:34:52] Found bcftools - /usr/local/bin/bcftools [07:34:52] Found samtools - /usr/local/bin/samtools [07:34:52] Found java - /usr/local/bin/java [07:34:52] Found snpEff - /usr/local/bin/snpEff [07:34:52] Found samclip - /usr/local/bin/samclip [07:34:52] Found seqtk - /usr/local/bin/seqtk [07:34:52] Found parallel - /usr/local/bin/parallel [07:34:52] Found freebayes - /usr/local/bin/freebayes [07:34:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:34:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:34:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:34:52] Found vcfuniq - /usr/local/bin/vcfuniq [07:34:52] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:34:52] Found gzip - /bin/gzip [07:34:52] Found vt - /usr/local/bin/vt [07:34:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:34:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:34:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:34:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:34:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:34:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:34:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:34:53] Please supply a reference FASTA/GBK/EMBL file with --reference
3[07:37:43] This is snippy 4.6.0
Show full stderr[07:37:43] This is snippy 4.6.0 [07:37:43] Written by Torsten Seemann [07:37:43] Obtained from https://github.com/tseemann/snippy [07:37:43] Detected operating system: linux [07:37:43] Enabling bundled linux tools. [07:37:43] Found bwa - /usr/local/bin/bwa [07:37:43] Found bcftools - /usr/local/bin/bcftools [07:37:43] Found samtools - /usr/local/bin/samtools [07:37:43] Found java - /usr/local/bin/java [07:37:43] Found snpEff - /usr/local/bin/snpEff [07:37:43] Found samclip - /usr/local/bin/samclip [07:37:43] Found seqtk - /usr/local/bin/seqtk [07:37:43] Found parallel - /usr/local/bin/parallel [07:37:43] Found freebayes - /usr/local/bin/freebayes [07:37:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:37:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:37:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:37:43] Found vcfuniq - /usr/local/bin/vcfuniq [07:37:43] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:37:43] Found gzip - /bin/gzip [07:37:43] Found vt - /usr/local/bin/vt [07:37:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:37:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:37:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:37:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:37:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:37:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:37:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:37:44] Please supply a reference FASTA/GBK/EMBL file with --reference
3[07:37:58] This is snippy 4.6.0
Show full stderr[07:37:58] This is snippy 4.6.0 [07:37:58] Written by Torsten Seemann [07:37:58] Obtained from https://github.com/tseemann/snippy [07:37:58] Detected operating system: linux [07:37:58] Enabling bundled linux tools. [07:37:58] Found bwa - /usr/local/bin/bwa [07:37:58] Found bcftools - /usr/local/bin/bcftools [07:37:58] Found samtools - /usr/local/bin/samtools [07:37:58] Found java - /usr/local/bin/java [07:37:58] Found snpEff - /usr/local/bin/snpEff [07:37:58] Found samclip - /usr/local/bin/samclip [07:37:58] Found seqtk - /usr/local/bin/seqtk [07:37:58] Found parallel - /usr/local/bin/parallel [07:37:58] Found freebayes - /usr/local/bin/freebayes [07:37:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:37:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:37:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:37:58] Found vcfuniq - /usr/local/bin/vcfuniq [07:37:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:37:58] Found gzip - /bin/gzip [07:37:58] Found vt - /usr/local/bin/vt [07:37:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:37:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:37:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:37:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:37:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:37:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:37:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:37:59] Please supply a reference FASTA/GBK/EMBL file with --reference
3[07:40:37] This is snippy 4.6.0
Show full stderr[07:40:37] This is snippy 4.6.0 [07:40:37] Written by Torsten Seemann [07:40:37] Obtained from https://github.com/tseemann/snippy [07:40:37] Detected operating system: linux [07:40:37] Enabling bundled linux tools. [07:40:37] Found bwa - /usr/local/bin/bwa [07:40:37] Found bcftools - /usr/local/bin/bcftools [07:40:37] Found samtools - /usr/local/bin/samtools [07:40:37] Found java - /usr/local/bin/java [07:40:37] Found snpEff - /usr/local/bin/snpEff [07:40:37] Found samclip - /usr/local/bin/samclip [07:40:37] Found seqtk - /usr/local/bin/seqtk [07:40:37] Found parallel - /usr/local/bin/parallel [07:40:37] Found freebayes - /usr/local/bin/freebayes [07:40:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:40:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:40:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:40:37] Found vcfuniq - /usr/local/bin/vcfuniq [07:40:37] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:40:37] Found gzip - /bin/gzip [07:40:37] Found vt - /usr/local/bin/vt [07:40:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:40:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:40:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:40:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:40:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:40:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:40:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:40:37] Please supply a reference FASTA/GBK/EMBL file with --reference
3[07:41:04] This is snippy 4.6.0
Show full stderr[07:41:04] This is snippy 4.6.0 [07:41:04] Written by Torsten Seemann [07:41:04] Obtained from https://github.com/tseemann/snippy [07:41:04] Detected operating system: linux [07:41:04] Enabling bundled linux tools. [07:41:04] Found bwa - /usr/local/bin/bwa [07:41:04] Found bcftools - /usr/local/bin/bcftools [07:41:04] Found samtools - /usr/local/bin/samtools [07:41:04] Found java - /usr/local/bin/java [07:41:04] Found snpEff - /usr/local/bin/snpEff [07:41:04] Found samclip - /usr/local/bin/samclip [07:41:04] Found seqtk - /usr/local/bin/seqtk [07:41:04] Found parallel - /usr/local/bin/parallel [07:41:04] Found freebayes - /usr/local/bin/freebayes [07:41:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:41:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:41:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:41:04] Found vcfuniq - /usr/local/bin/vcfuniq [07:41:04] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:41:04] Found gzip - /bin/gzip [07:41:04] Found vt - /usr/local/bin/vt [07:41:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:41:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:41:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:41:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:41:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:41:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:41:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:41:04] Please supply a reference FASTA/GBK/EMBL file with --reference
3[07:44:16] This is snippy 4.6.0
Show full stderr[07:44:16] This is snippy 4.6.0 [07:44:16] Written by Torsten Seemann [07:44:16] Obtained from https://github.com/tseemann/snippy [07:44:16] Detected operating system: linux [07:44:16] Enabling bundled linux tools. [07:44:16] Found bwa - /usr/local/bin/bwa [07:44:16] Found bcftools - /usr/local/bin/bcftools [07:44:16] Found samtools - /usr/local/bin/samtools [07:44:16] Found java - /usr/local/bin/java [07:44:16] Found snpEff - /usr/local/bin/snpEff [07:44:16] Found samclip - /usr/local/bin/samclip [07:44:16] Found seqtk - /usr/local/bin/seqtk [07:44:16] Found parallel - /usr/local/bin/parallel [07:44:16] Found freebayes - /usr/local/bin/freebayes [07:44:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:44:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:44:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:44:16] Found vcfuniq - /usr/local/bin/vcfuniq [07:44:16] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:44:16] Found gzip - /bin/gzip [07:44:16] Found vt - /usr/local/bin/vt [07:44:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:44:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:44:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:44:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:44:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:44:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:44:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:44:17] Please supply a reference FASTA/GBK/EMBL file with --reference
3[07:47:13] This is snippy 4.6.0
Show full stderr[07:47:13] This is snippy 4.6.0 [07:47:13] Written by Torsten Seemann [07:47:13] Obtained from https://github.com/tseemann/snippy [07:47:13] Detected operating system: linux [07:47:13] Enabling bundled linux tools. [07:47:13] Found bwa - /usr/local/bin/bwa [07:47:13] Found bcftools - /usr/local/bin/bcftools [07:47:13] Found samtools - /usr/local/bin/samtools [07:47:13] Found java - /usr/local/bin/java [07:47:13] Found snpEff - /usr/local/bin/snpEff [07:47:13] Found samclip - /usr/local/bin/samclip [07:47:13] Found seqtk - /usr/local/bin/seqtk [07:47:13] Found parallel - /usr/local/bin/parallel [07:47:13] Found freebayes - /usr/local/bin/freebayes [07:47:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:47:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:47:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:47:13] Found vcfuniq - /usr/local/bin/vcfuniq [07:47:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:47:13] Found gzip - /bin/gzip [07:47:13] Found vt - /usr/local/bin/vt [07:47:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:47:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:47:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:47:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:47:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:47:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:47:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:47:14] Please supply a reference FASTA/GBK/EMBL file with --reference
3[07:47:28] This is snippy 4.6.0
Show full stderr[07:47:28] This is snippy 4.6.0 [07:47:28] Written by Torsten Seemann [07:47:28] Obtained from https://github.com/tseemann/snippy [07:47:28] Detected operating system: linux [07:47:28] Enabling bundled linux tools. [07:47:28] Found bwa - /usr/local/bin/bwa [07:47:28] Found bcftools - /usr/local/bin/bcftools [07:47:28] Found samtools - /usr/local/bin/samtools [07:47:28] Found java - /usr/local/bin/java [07:47:28] Found snpEff - /usr/local/bin/snpEff [07:47:28] Found samclip - /usr/local/bin/samclip [07:47:28] Found seqtk - /usr/local/bin/seqtk [07:47:28] Found parallel - /usr/local/bin/parallel [07:47:28] Found freebayes - /usr/local/bin/freebayes [07:47:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:47:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:47:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:47:28] Found vcfuniq - /usr/local/bin/vcfuniq [07:47:28] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:47:28] Found gzip - /bin/gzip [07:47:28] Found vt - /usr/local/bin/vt [07:47:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:47:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:47:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:47:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:47:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:47:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:47:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:47:29] Please supply a reference FASTA/GBK/EMBL file with --reference
3[04:43:22] This is snippy 4.6.0
Show full stderr[04:43:22] This is snippy 4.6.0 [04:43:22] Written by Torsten Seemann [04:43:22] Obtained from https://github.com/tseemann/snippy [04:43:22] Detected operating system: linux [04:43:22] Enabling bundled linux tools. [04:43:22] Found bwa - /usr/local/bin/bwa [04:43:22] Found bcftools - /usr/local/bin/bcftools [04:43:22] Found samtools - /usr/local/bin/samtools [04:43:22] Found java - /usr/local/bin/java [04:43:22] Found snpEff - /usr/local/bin/snpEff [04:43:22] Found samclip - /usr/local/bin/samclip [04:43:22] Found seqtk - /usr/local/bin/seqtk [04:43:22] Found parallel - /usr/local/bin/parallel [04:43:22] Found freebayes - /usr/local/bin/freebayes [04:43:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:43:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:43:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:43:22] Found vcfuniq - /usr/local/bin/vcfuniq [04:43:22] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:43:22] Found gzip - /bin/gzip [04:43:22] Found vt - /usr/local/bin/vt [04:43:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:43:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:43:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:43:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:43:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:43:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:43:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:43:23] Please supply a reference FASTA/GBK/EMBL file with --reference
3[12:48:43] This is snippy 4.6.0
Show full stderr[12:48:43] This is snippy 4.6.0 [12:48:43] Written by Torsten Seemann [12:48:43] Obtained from https://github.com/tseemann/snippy [12:48:43] Detected operating system: linux [12:48:43] Enabling bundled linux tools. [12:48:43] Found bwa - /usr/local/bin/bwa [12:48:43] Found bcftools - /usr/local/bin/bcftools [12:48:43] Found samtools - /usr/local/bin/samtools [12:48:43] Found java - /usr/local/bin/java [12:48:43] Found snpEff - /usr/local/bin/snpEff [12:48:43] Found samclip - /usr/local/bin/samclip [12:48:43] Found seqtk - /usr/local/bin/seqtk [12:48:43] Found parallel - /usr/local/bin/parallel [12:48:43] Found freebayes - /usr/local/bin/freebayes [12:48:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:48:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:48:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:48:43] Found vcfuniq - /usr/local/bin/vcfuniq [12:48:43] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:48:43] Found gzip - /bin/gzip [12:48:43] Found vt - /usr/local/bin/vt [12:48:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:48:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:48:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:48:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:48:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:48:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:48:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:48:44] Please supply a reference FASTA/GBK/EMBL file with --reference
3[12:59:35] This is snippy 4.6.0
Show full stderr[12:59:35] This is snippy 4.6.0 [12:59:35] Written by Torsten Seemann [12:59:35] Obtained from https://github.com/tseemann/snippy [12:59:35] Detected operating system: linux [12:59:35] Enabling bundled linux tools. [12:59:35] Found bwa - /usr/local/bin/bwa [12:59:35] Found bcftools - /usr/local/bin/bcftools [12:59:35] Found samtools - /usr/local/bin/samtools [12:59:35] Found java - /usr/local/bin/java [12:59:35] Found snpEff - /usr/local/bin/snpEff [12:59:35] Found samclip - /usr/local/bin/samclip [12:59:35] Found seqtk - /usr/local/bin/seqtk [12:59:35] Found parallel - /usr/local/bin/parallel [12:59:35] Found freebayes - /usr/local/bin/freebayes [12:59:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:59:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:59:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:59:35] Found vcfuniq - /usr/local/bin/vcfuniq [12:59:35] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:59:35] Found gzip - /bin/gzip [12:59:35] Found vt - /usr/local/bin/vt [12:59:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:59:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:59:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:59:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:59:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:59:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:59:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:59:36] Please supply a reference FASTA/GBK/EMBL file with --reference
3[19:40:39] This is snippy 4.6.0
Show full stderr[19:40:39] This is snippy 4.6.0 [19:40:39] Written by Torsten Seemann [19:40:39] Obtained from https://github.com/tseemann/snippy [19:40:39] Detected operating system: linux [19:40:39] Enabling bundled linux tools. [19:40:39] Found bwa - /usr/local/bin/bwa [19:40:39] Found bcftools - /usr/local/bin/bcftools [19:40:39] Found samtools - /usr/local/bin/samtools [19:40:39] Found java - /usr/local/bin/java [19:40:39] Found snpEff - /usr/local/bin/snpEff [19:40:39] Found samclip - /usr/local/bin/samclip [19:40:39] Found seqtk - /usr/local/bin/seqtk [19:40:39] Found parallel - /usr/local/bin/parallel [19:40:39] Found freebayes - /usr/local/bin/freebayes [19:40:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [19:40:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [19:40:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [19:40:39] Found vcfuniq - /usr/local/bin/vcfuniq [19:40:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [19:40:39] Found gzip - /bin/gzip [19:40:39] Found vt - /usr/local/bin/vt [19:40:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [19:40:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [19:40:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [19:40:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [19:40:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [19:40:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [19:40:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [19:40:40] Please supply a reference FASTA/GBK/EMBL file with --reference
3[14:45:15] This is snippy 4.6.0
Show full stderr[14:45:15] This is snippy 4.6.0 [14:45:15] Written by Torsten Seemann [14:45:15] Obtained from https://github.com/tseemann/snippy [14:45:15] Detected operating system: linux [14:45:15] Enabling bundled linux tools. [14:45:15] Found bwa - /usr/local/bin/bwa [14:45:15] Found bcftools - /usr/local/bin/bcftools [14:45:15] Found samtools - /usr/local/bin/samtools [14:45:15] Found java - /usr/local/bin/java [14:45:15] Found snpEff - /usr/local/bin/snpEff [14:45:15] Found samclip - /usr/local/bin/samclip [14:45:15] Found seqtk - /usr/local/bin/seqtk [14:45:15] Found parallel - /usr/local/bin/parallel [14:45:15] Found freebayes - /usr/local/bin/freebayes [14:45:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:45:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:45:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:45:15] Found vcfuniq - /usr/local/bin/vcfuniq [14:45:15] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:45:15] Found gzip - /bin/gzip [14:45:15] Found vt - /usr/local/bin/vt [14:45:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:45:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:45:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:45:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:45:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:45:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:45:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:45:16] Please supply a reference FASTA/GBK/EMBL file with --reference
3[14:46:45] This is snippy 4.6.0
Show full stderr[14:46:45] This is snippy 4.6.0 [14:46:45] Written by Torsten Seemann [14:46:45] Obtained from https://github.com/tseemann/snippy [14:46:45] Detected operating system: linux [14:46:45] Enabling bundled linux tools. [14:46:45] Found bwa - /usr/local/bin/bwa [14:46:45] Found bcftools - /usr/local/bin/bcftools [14:46:45] Found samtools - /usr/local/bin/samtools [14:46:45] Found java - /usr/local/bin/java [14:46:45] Found snpEff - /usr/local/bin/snpEff [14:46:45] Found samclip - /usr/local/bin/samclip [14:46:45] Found seqtk - /usr/local/bin/seqtk [14:46:45] Found parallel - /usr/local/bin/parallel [14:46:45] Found freebayes - /usr/local/bin/freebayes [14:46:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:46:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:46:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:46:45] Found vcfuniq - /usr/local/bin/vcfuniq [14:46:45] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:46:45] Found gzip - /bin/gzip [14:46:45] Found vt - /usr/local/bin/vt [14:46:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:46:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:46:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:46:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:46:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:46:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:46:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:46:46] Please supply a reference FASTA/GBK/EMBL file with --reference
3[14:51:54] This is snippy 4.6.0
Show full stderr[14:51:54] This is snippy 4.6.0 [14:51:54] Written by Torsten Seemann [14:51:54] Obtained from https://github.com/tseemann/snippy [14:51:54] Detected operating system: linux [14:51:54] Enabling bundled linux tools. [14:51:54] Found bwa - /usr/local/bin/bwa [14:51:54] Found bcftools - /usr/local/bin/bcftools [14:51:54] Found samtools - /usr/local/bin/samtools [14:51:54] Found java - /usr/local/bin/java [14:51:54] Found snpEff - /usr/local/bin/snpEff [14:51:54] Found samclip - /usr/local/bin/samclip [14:51:54] Found seqtk - /usr/local/bin/seqtk [14:51:54] Found parallel - /usr/local/bin/parallel [14:51:54] Found freebayes - /usr/local/bin/freebayes [14:51:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:51:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:51:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:51:54] Found vcfuniq - /usr/local/bin/vcfuniq [14:51:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:51:54] Found gzip - /bin/gzip [14:51:54] Found vt - /usr/local/bin/vt [14:51:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:51:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:51:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:51:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:51:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:51:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:51:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:51:55] Please supply a reference FASTA/GBK/EMBL file with --reference
3[14:46:30] This is snippy 4.6.0
Show full stderr[14:46:30] This is snippy 4.6.0 [14:46:30] Written by Torsten Seemann [14:46:30] Obtained from https://github.com/tseemann/snippy [14:46:30] Detected operating system: linux [14:46:30] Enabling bundled linux tools. [14:46:30] Found bwa - /usr/local/bin/bwa [14:46:30] Found bcftools - /usr/local/bin/bcftools [14:46:30] Found samtools - /usr/local/bin/samtools [14:46:30] Found java - /usr/local/bin/java [14:46:30] Found snpEff - /usr/local/bin/snpEff [14:46:30] Found samclip - /usr/local/bin/samclip [14:46:30] Found seqtk - /usr/local/bin/seqtk [14:46:30] Found parallel - /usr/local/bin/parallel [14:46:30] Found freebayes - /usr/local/bin/freebayes [14:46:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:46:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:46:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:46:30] Found vcfuniq - /usr/local/bin/vcfuniq [14:46:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:46:30] Found gzip - /bin/gzip [14:46:30] Found vt - /usr/local/bin/vt [14:46:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:46:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:46:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:46:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:46:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:46:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:46:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:46:31] Please supply a reference FASTA/GBK/EMBL file with --reference
3[14:47:39] This is snippy 4.6.0
Show full stderr[14:47:39] This is snippy 4.6.0 [14:47:39] Written by Torsten Seemann [14:47:39] Obtained from https://github.com/tseemann/snippy [14:47:39] Detected operating system: linux [14:47:39] Enabling bundled linux tools. [14:47:39] Found bwa - /usr/local/bin/bwa [14:47:39] Found bcftools - /usr/local/bin/bcftools [14:47:39] Found samtools - /usr/local/bin/samtools [14:47:39] Found java - /usr/local/bin/java [14:47:39] Found snpEff - /usr/local/bin/snpEff [14:47:39] Found samclip - /usr/local/bin/samclip [14:47:39] Found seqtk - /usr/local/bin/seqtk [14:47:39] Found parallel - /usr/local/bin/parallel [14:47:39] Found freebayes - /usr/local/bin/freebayes [14:47:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:47:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:47:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:47:39] Found vcfuniq - /usr/local/bin/vcfuniq [14:47:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:47:39] Found gzip - /bin/gzip [14:47:39] Found vt - /usr/local/bin/vt [14:47:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:47:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:47:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:47:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:47:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:47:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:47:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:47:40] Please supply a reference FASTA/GBK/EMBL file with --reference
3[14:52:38] This is snippy 4.6.0
Show full stderr[14:52:38] This is snippy 4.6.0 [14:52:38] Written by Torsten Seemann [14:52:38] Obtained from https://github.com/tseemann/snippy [14:52:38] Detected operating system: linux [14:52:38] Enabling bundled linux tools. [14:52:38] Found bwa - /usr/local/bin/bwa [14:52:38] Found bcftools - /usr/local/bin/bcftools [14:52:38] Found samtools - /usr/local/bin/samtools [14:52:38] Found java - /usr/local/bin/java [14:52:38] Found snpEff - /usr/local/bin/snpEff [14:52:38] Found samclip - /usr/local/bin/samclip [14:52:38] Found seqtk - /usr/local/bin/seqtk [14:52:38] Found parallel - /usr/local/bin/parallel [14:52:38] Found freebayes - /usr/local/bin/freebayes [14:52:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:52:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:52:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:52:38] Found vcfuniq - /usr/local/bin/vcfuniq [14:52:38] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:52:38] Found gzip - /bin/gzip [14:52:38] Found vt - /usr/local/bin/vt [14:52:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:52:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:52:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:52:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:52:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:52:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:52:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:52:39] Please supply a reference FASTA/GBK/EMBL file with --reference
3[14:52:53] This is snippy 4.6.0
Show full stderr[14:52:53] This is snippy 4.6.0 [14:52:53] Written by Torsten Seemann [14:52:53] Obtained from https://github.com/tseemann/snippy [14:52:53] Detected operating system: linux [14:52:53] Enabling bundled linux tools. [14:52:53] Found bwa - /usr/local/bin/bwa [14:52:53] Found bcftools - /usr/local/bin/bcftools [14:52:53] Found samtools - /usr/local/bin/samtools [14:52:53] Found java - /usr/local/bin/java [14:52:53] Found snpEff - /usr/local/bin/snpEff [14:52:53] Found samclip - /usr/local/bin/samclip [14:52:53] Found seqtk - /usr/local/bin/seqtk [14:52:53] Found parallel - /usr/local/bin/parallel [14:52:53] Found freebayes - /usr/local/bin/freebayes [14:52:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:52:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:52:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:52:53] Found vcfuniq - /usr/local/bin/vcfuniq [14:52:53] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:52:53] Found gzip - /bin/gzip [14:52:53] Found vt - /usr/local/bin/vt [14:52:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:52:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:52:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:52:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:52:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:52:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:52:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:52:53] Please supply a reference FASTA/GBK/EMBL file with --reference
3[17:30:18] This is snippy 4.6.0
Show full stderr[17:30:18] This is snippy 4.6.0 [17:30:18] Written by Torsten Seemann [17:30:18] Obtained from https://github.com/tseemann/snippy [17:30:18] Detected operating system: linux [17:30:18] Enabling bundled linux tools. [17:30:18] Found bwa - /usr/local/bin/bwa [17:30:18] Found bcftools - /usr/local/bin/bcftools [17:30:18] Found samtools - /usr/local/bin/samtools [17:30:18] Found java - /usr/local/bin/java [17:30:18] Found snpEff - /usr/local/bin/snpEff [17:30:18] Found samclip - /usr/local/bin/samclip [17:30:18] Found seqtk - /usr/local/bin/seqtk [17:30:18] Found parallel - /usr/local/bin/parallel [17:30:18] Found freebayes - /usr/local/bin/freebayes [17:30:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:30:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:30:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:30:19] Found vcfuniq - /usr/local/bin/vcfuniq [17:30:19] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:30:19] Found gzip - /bin/gzip [17:30:19] Found vt - /usr/local/bin/vt [17:30:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:30:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:30:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:30:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:30:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:30:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:30:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:30:23] Please supply a reference FASTA/GBK/EMBL file with --reference
3[17:42:52] This is snippy 4.6.0
Show full stderr[17:42:52] This is snippy 4.6.0 [17:42:52] Written by Torsten Seemann [17:42:52] Obtained from https://github.com/tseemann/snippy [17:42:52] Detected operating system: linux [17:42:52] Enabling bundled linux tools. [17:42:52] Found bwa - /usr/local/bin/bwa [17:42:52] Found bcftools - /usr/local/bin/bcftools [17:42:52] Found samtools - /usr/local/bin/samtools [17:42:52] Found java - /usr/local/bin/java [17:42:52] Found snpEff - /usr/local/bin/snpEff [17:42:52] Found samclip - /usr/local/bin/samclip [17:42:52] Found seqtk - /usr/local/bin/seqtk [17:42:52] Found parallel - /usr/local/bin/parallel [17:42:52] Found freebayes - /usr/local/bin/freebayes [17:42:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:42:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:42:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:42:52] Found vcfuniq - /usr/local/bin/vcfuniq [17:42:52] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:42:52] Found gzip - /bin/gzip [17:42:52] Found vt - /usr/local/bin/vt [17:42:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:42:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:42:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:42:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:42:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:42:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:42:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:42:53] Please supply a reference FASTA/GBK/EMBL file with --reference
3[17:36:36] This is snippy 4.6.0
Show full stderr[17:36:36] This is snippy 4.6.0 [17:36:36] Written by Torsten Seemann [17:36:36] Obtained from https://github.com/tseemann/snippy [17:36:36] Detected operating system: linux [17:36:36] Enabling bundled linux tools. [17:36:36] Found bwa - /usr/local/bin/bwa [17:36:36] Found bcftools - /usr/local/bin/bcftools [17:36:36] Found samtools - /usr/local/bin/samtools [17:36:36] Found java - /usr/local/bin/java [17:36:36] Found snpEff - /usr/local/bin/snpEff [17:36:36] Found samclip - /usr/local/bin/samclip [17:36:36] Found seqtk - /usr/local/bin/seqtk [17:36:36] Found parallel - /usr/local/bin/parallel [17:36:36] Found freebayes - /usr/local/bin/freebayes [17:36:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:36:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:36:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:36:36] Found vcfuniq - /usr/local/bin/vcfuniq [17:36:36] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:36:36] Found gzip - /bin/gzip [17:36:36] Found vt - /usr/local/bin/vt [17:36:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:36:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:36:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:36:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:36:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:36:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:36:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:36:43] Please supply a reference FASTA/GBK/EMBL file with --reference
3[17:37:39] This is snippy 4.6.0
Show full stderr[17:37:39] This is snippy 4.6.0 [17:37:39] Written by Torsten Seemann [17:37:39] Obtained from https://github.com/tseemann/snippy [17:37:39] Detected operating system: linux [17:37:39] Enabling bundled linux tools. [17:37:39] Found bwa - /usr/local/bin/bwa [17:37:39] Found bcftools - /usr/local/bin/bcftools [17:37:39] Found samtools - /usr/local/bin/samtools [17:37:39] Found java - /usr/local/bin/java [17:37:39] Found snpEff - /usr/local/bin/snpEff [17:37:39] Found samclip - /usr/local/bin/samclip [17:37:39] Found seqtk - /usr/local/bin/seqtk [17:37:39] Found parallel - /usr/local/bin/parallel [17:37:39] Found freebayes - /usr/local/bin/freebayes [17:37:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:37:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:37:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:37:39] Found vcfuniq - /usr/local/bin/vcfuniq [17:37:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:37:39] Found gzip - /bin/gzip [17:37:39] Found vt - /usr/local/bin/vt [17:37:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:37:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:37:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:37:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:37:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:37:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:37:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:37:39] Please supply a reference FASTA/GBK/EMBL file with --reference
3[17:38:19] This is snippy 4.6.0
Show full stderr[17:38:19] This is snippy 4.6.0 [17:38:19] Written by Torsten Seemann [17:38:19] Obtained from https://github.com/tseemann/snippy [17:38:19] Detected operating system: linux [17:38:19] Enabling bundled linux tools. [17:38:19] Found bwa - /usr/local/bin/bwa [17:38:19] Found bcftools - /usr/local/bin/bcftools [17:38:19] Found samtools - /usr/local/bin/samtools [17:38:19] Found java - /usr/local/bin/java [17:38:19] Found snpEff - /usr/local/bin/snpEff [17:38:19] Found samclip - /usr/local/bin/samclip [17:38:19] Found seqtk - /usr/local/bin/seqtk [17:38:19] Found parallel - /usr/local/bin/parallel [17:38:19] Found freebayes - /usr/local/bin/freebayes [17:38:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:38:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:38:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:38:19] Found vcfuniq - /usr/local/bin/vcfuniq [17:38:19] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:38:19] Found gzip - /bin/gzip [17:38:19] Found vt - /usr/local/bin/vt [17:38:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:38:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:38:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:38:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:38:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:38:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:38:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:38:19] Please supply a reference FASTA/GBK/EMBL file with --reference
3[17:38:07] This is snippy 4.6.0
Show full stderr[17:38:07] This is snippy 4.6.0 [17:38:07] Written by Torsten Seemann [17:38:07] Obtained from https://github.com/tseemann/snippy [17:38:07] Detected operating system: linux [17:38:07] Enabling bundled linux tools. [17:38:07] Found bwa - /usr/local/bin/bwa [17:38:07] Found bcftools - /usr/local/bin/bcftools [17:38:07] Found samtools - /usr/local/bin/samtools [17:38:07] Found java - /usr/local/bin/java [17:38:07] Found snpEff - /usr/local/bin/snpEff [17:38:07] Found samclip - /usr/local/bin/samclip [17:38:07] Found seqtk - /usr/local/bin/seqtk [17:38:07] Found parallel - /usr/local/bin/parallel [17:38:07] Found freebayes - /usr/local/bin/freebayes [17:38:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:38:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:38:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:38:07] Found vcfuniq - /usr/local/bin/vcfuniq [17:38:07] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:38:07] Found gzip - /bin/gzip [17:38:07] Found vt - /usr/local/bin/vt [17:38:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:38:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:38:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:38:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:38:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:38:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:38:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:38:07] Please supply a reference FASTA/GBK/EMBL file with --reference
3[00:33:27] This is snippy 4.6.0
Show full stderr[00:33:27] This is snippy 4.6.0 [00:33:27] Written by Torsten Seemann [00:33:27] Obtained from https://github.com/tseemann/snippy [00:33:27] Detected operating system: linux [00:33:27] Enabling bundled linux tools. [00:33:27] Found bwa - /usr/local/bin/bwa [00:33:27] Found bcftools - /usr/local/bin/bcftools [00:33:27] Found samtools - /usr/local/bin/samtools [00:33:27] Found java - /usr/local/bin/java [00:33:27] Found snpEff - /usr/local/bin/snpEff [00:33:27] Found samclip - /usr/local/bin/samclip [00:33:27] Found seqtk - /usr/local/bin/seqtk [00:33:27] Found parallel - /usr/local/bin/parallel [00:33:27] Found freebayes - /usr/local/bin/freebayes [00:33:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:33:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:33:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:33:27] Found vcfuniq - /usr/local/bin/vcfuniq [00:33:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:33:27] Found gzip - /bin/gzip [00:33:27] Found vt - /usr/local/bin/vt [00:33:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:33:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:33:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:33:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:33:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:33:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:33:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:33:28] Please supply a reference FASTA/GBK/EMBL file with --reference
3[00:54:26] This is snippy 4.6.0
Show full stderr[00:54:26] This is snippy 4.6.0 [00:54:26] Written by Torsten Seemann [00:54:26] Obtained from https://github.com/tseemann/snippy [00:54:26] Detected operating system: linux [00:54:26] Enabling bundled linux tools. [00:54:26] Found bwa - /usr/local/bin/bwa [00:54:26] Found bcftools - /usr/local/bin/bcftools [00:54:26] Found samtools - /usr/local/bin/samtools [00:54:26] Found java - /usr/local/bin/java [00:54:26] Found snpEff - /usr/local/bin/snpEff [00:54:26] Found samclip - /usr/local/bin/samclip [00:54:26] Found seqtk - /usr/local/bin/seqtk [00:54:26] Found parallel - /usr/local/bin/parallel [00:54:26] Found freebayes - /usr/local/bin/freebayes [00:54:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:54:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:54:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:54:26] Found vcfuniq - /usr/local/bin/vcfuniq [00:54:26] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:54:26] Found gzip - /bin/gzip [00:54:26] Found vt - /usr/local/bin/vt [00:54:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:54:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:54:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:54:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:54:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:54:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:54:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:54:27] Please supply a reference FASTA/GBK/EMBL file with --reference
3[08:55:04] This is snippy 4.6.0
Show full stderr[08:55:04] This is snippy 4.6.0 [08:55:04] Written by Torsten Seemann [08:55:04] Obtained from https://github.com/tseemann/snippy [08:55:04] Detected operating system: linux [08:55:04] Enabling bundled linux tools. [08:55:04] Found bwa - /usr/local/bin/bwa [08:55:04] Found bcftools - /usr/local/bin/bcftools [08:55:04] Found samtools - /usr/local/bin/samtools [08:55:04] Found java - /usr/local/bin/java [08:55:04] Found snpEff - /usr/local/bin/snpEff [08:55:04] Found samclip - /usr/local/bin/samclip [08:55:04] Found seqtk - /usr/local/bin/seqtk [08:55:04] Found parallel - /usr/local/bin/parallel [08:55:04] Found freebayes - /usr/local/bin/freebayes [08:55:05] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:55:05] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:55:05] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:55:05] Found vcfuniq - /usr/local/bin/vcfuniq [08:55:05] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:55:05] Found gzip - /bin/gzip [08:55:05] Found vt - /usr/local/bin/vt [08:55:05] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:55:05] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:55:05] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:55:05] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:55:05] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:55:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:55:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:55:06] Using reference: /corral4/main/objects/8/5/7/dataset_85795cef-4d28-485e-8eef-1c59399f6e13.dat [08:55:09] Treating reference as 'genbank' format. [08:55:09] Will use 1 CPU cores. [08:55:09] Using read file: /corral4/main/objects/b/4/0/dataset_b4066cae-0670-4b65-9b32-348e22fbe97f.dat [08:55:09] Creating folder: PAK_resistant_Strain_zip [08:55:09] Changing working directory: PAK_resistant_Strain_zip [08:55:09] Creating reference folder: reference [08:55:09] Extracting FASTA and GFF from reference. [08:55:13] Wrote 1 sequences to ref.fa [08:55:13] Wrote 5867 features to ref.gff [08:55:13] Creating reference/snpeff.config [08:55:13] Freebayes will process 1 chunks of 6502546 bp, 1 chunks at a time. [08:55:13] Using BAM RG (Read Group) ID: PAK_resistant_Strain_zip [08:55:13] Running: samtools faidx reference/ref.fa 2>> snps.log [08:55:14] Running: bwa index reference/ref.fa 2>> snps.log [08:55:21] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [08:55:22] Running: ln -sf reference/ref.fa . 2>> snps.log [08:55:22] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [08:55:23] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [08:55:23] Running: snpEff build -c reference/snpeff.config -dataDir . -gff3 ref 2>> snps.log [08:55:33] Running: bwa mem -Y -M -R '@RG\tID:PAK_resistant_Strain_zip\tSM:PAK_resistant_Strain_zip' -t 1 reference/ref.fa /corral4/main/objects/b/4/0/dataset_b4066cae-0670-4b65-9b32-348e22fbe97f.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/073/013/73013863/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/073/013/73013863/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/073/013/73013863/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 1 sequences in reference/ref.fa.fai [M::bwa_idx_load_from_di
3[21:23:50] This is snippy 4.6.0
Show full stderr[21:23:50] This is snippy 4.6.0 [21:23:50] Written by Torsten Seemann [21:23:50] Obtained from https://github.com/tseemann/snippy [21:23:50] Detected operating system: linux [21:23:50] Enabling bundled linux tools. [21:23:50] Found bwa - /usr/local/bin/bwa [21:23:50] Found bcftools - /usr/local/bin/bcftools [21:23:50] Found samtools - /usr/local/bin/samtools [21:23:50] Found java - /usr/local/bin/java [21:23:50] Found snpEff - /usr/local/bin/snpEff [21:23:50] Found samclip - /usr/local/bin/samclip [21:23:50] Found seqtk - /usr/local/bin/seqtk [21:23:50] Found parallel - /usr/local/bin/parallel [21:23:50] Found freebayes - /usr/local/bin/freebayes [21:23:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:23:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:23:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:23:50] Found vcfuniq - /usr/local/bin/vcfuniq [21:23:50] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:23:50] Found gzip - /bin/gzip [21:23:50] Found vt - /usr/local/bin/vt [21:23:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:23:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:23:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:23:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:23:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:23:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:23:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:23:51] Please supply a reference FASTA/GBK/EMBL file with --reference
3[05:02:17] This is snippy 4.6.0
Show full stderr[05:02:17] This is snippy 4.6.0 [05:02:17] Written by Torsten Seemann [05:02:17] Obtained from https://github.com/tseemann/snippy [05:02:17] Detected operating system: linux [05:02:17] Enabling bundled linux tools. [05:02:17] Found bwa - /usr/local/bin/bwa [05:02:17] Found bcftools - /usr/local/bin/bcftools [05:02:17] Found samtools - /usr/local/bin/samtools [05:02:17] Found java - /usr/local/bin/java [05:02:17] Found snpEff - /usr/local/bin/snpEff [05:02:17] Found samclip - /usr/local/bin/samclip [05:02:17] Found seqtk - /usr/local/bin/seqtk [05:02:17] Found parallel - /usr/local/bin/parallel [05:02:17] Found freebayes - /usr/local/bin/freebayes [05:02:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:02:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:02:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:02:17] Found vcfuniq - /usr/local/bin/vcfuniq [05:02:17] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:02:17] Found gzip - /bin/gzip [05:02:17] Found vt - /usr/local/bin/vt [05:02:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:02:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:02:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:02:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:02:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:02:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:02:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:02:18] Please supply a reference FASTA/GBK/EMBL file with --reference
2[21:23:38] This is snippy 4.6.0
Show full stderr[21:23:38] This is snippy 4.6.0 [21:23:38] Written by Torsten Seemann [21:23:38] Obtained from https://github.com/tseemann/snippy [21:23:38] Detected operating system: linux [21:23:38] Enabling bundled linux tools. [21:23:38] Found bwa - /usr/local/bin/bwa [21:23:38] Found bcftools - /usr/local/bin/bcftools [21:23:38] Found samtools - /usr/local/bin/samtools [21:23:38] Found java - /usr/local/bin/java [21:23:38] Found snpEff - /usr/local/bin/snpEff [21:23:38] Found samclip - /usr/local/bin/samclip [21:23:38] Found seqtk - /usr/local/bin/seqtk [21:23:38] Found parallel - /usr/local/bin/parallel [21:23:38] Found freebayes - /usr/local/bin/freebayes [21:23:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:23:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:23:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:23:38] Found vcfuniq - /usr/local/bin/vcfuniq [21:23:38] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:23:38] Found gzip - /bin/gzip [21:23:38] Found vt - /usr/local/bin/vt [21:23:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:23:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:23:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:23:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:23:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:23:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:23:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:23:41] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat [21:23:42] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat'
2[21:23:52] This is snippy 4.6.0
Show full stderr[21:23:52] This is snippy 4.6.0 [21:23:52] Written by Torsten Seemann [21:23:52] Obtained from https://github.com/tseemann/snippy [21:23:52] Detected operating system: linux [21:23:52] Enabling bundled linux tools. [21:23:52] Found bwa - /usr/local/bin/bwa [21:23:52] Found bcftools - /usr/local/bin/bcftools [21:23:52] Found samtools - /usr/local/bin/samtools [21:23:52] Found java - /usr/local/bin/java [21:23:52] Found snpEff - /usr/local/bin/snpEff [21:23:52] Found samclip - /usr/local/bin/samclip [21:23:52] Found seqtk - /usr/local/bin/seqtk [21:23:52] Found parallel - /usr/local/bin/parallel [21:23:52] Found freebayes - /usr/local/bin/freebayes [21:23:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:23:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:23:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:23:52] Found vcfuniq - /usr/local/bin/vcfuniq [21:23:53] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:23:53] Found gzip - /bin/gzip [21:23:53] Found vt - /usr/local/bin/vt [21:23:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:23:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:23:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:23:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:23:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:23:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:23:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:23:54] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat [21:23:54] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat'
2[21:23:55] This is snippy 4.6.0
Show full stderr[21:23:55] This is snippy 4.6.0 [21:23:55] Written by Torsten Seemann [21:23:55] Obtained from https://github.com/tseemann/snippy [21:23:55] Detected operating system: linux [21:23:55] Enabling bundled linux tools. [21:23:55] Found bwa - /usr/local/bin/bwa [21:23:55] Found bcftools - /usr/local/bin/bcftools [21:23:55] Found samtools - /usr/local/bin/samtools [21:23:55] Found java - /usr/local/bin/java [21:23:55] Found snpEff - /usr/local/bin/snpEff [21:23:55] Found samclip - /usr/local/bin/samclip [21:23:55] Found seqtk - /usr/local/bin/seqtk [21:23:55] Found parallel - /usr/local/bin/parallel [21:23:56] Found freebayes - /usr/local/bin/freebayes [21:23:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:23:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:23:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:23:56] Found vcfuniq - /usr/local/bin/vcfuniq [21:23:56] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:23:56] Found gzip - /bin/gzip [21:23:56] Found vt - /usr/local/bin/vt [21:23:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:23:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:23:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:23:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:23:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:23:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:23:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:23:57] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat [21:23:57] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat'
2[21:24:27] This is snippy 4.6.0
Show full stderr[21:24:27] This is snippy 4.6.0 [21:24:27] Written by Torsten Seemann [21:24:27] Obtained from https://github.com/tseemann/snippy [21:24:27] Detected operating system: linux [21:24:27] Enabling bundled linux tools. [21:24:27] Found bwa - /usr/local/bin/bwa [21:24:27] Found bcftools - /usr/local/bin/bcftools [21:24:27] Found samtools - /usr/local/bin/samtools [21:24:27] Found java - /usr/local/bin/java [21:24:27] Found snpEff - /usr/local/bin/snpEff [21:24:27] Found samclip - /usr/local/bin/samclip [21:24:27] Found seqtk - /usr/local/bin/seqtk [21:24:27] Found parallel - /usr/local/bin/parallel [21:24:27] Found freebayes - /usr/local/bin/freebayes [21:24:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:24:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:24:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:24:27] Found vcfuniq - /usr/local/bin/vcfuniq [21:24:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:24:27] Found gzip - /bin/gzip [21:24:27] Found vt - /usr/local/bin/vt [21:24:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:24:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:24:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:24:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:24:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:24:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:24:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:24:28] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat [21:24:28] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat'
2[21:24:08] This is snippy 4.6.0
Show full stderr[21:24:08] This is snippy 4.6.0 [21:24:08] Written by Torsten Seemann [21:24:08] Obtained from https://github.com/tseemann/snippy [21:24:08] Detected operating system: linux [21:24:08] Enabling bundled linux tools. [21:24:08] Found bwa - /usr/local/bin/bwa [21:24:08] Found bcftools - /usr/local/bin/bcftools [21:24:08] Found samtools - /usr/local/bin/samtools [21:24:08] Found java - /usr/local/bin/java [21:24:08] Found snpEff - /usr/local/bin/snpEff [21:24:08] Found samclip - /usr/local/bin/samclip [21:24:08] Found seqtk - /usr/local/bin/seqtk [21:24:08] Found parallel - /usr/local/bin/parallel [21:24:08] Found freebayes - /usr/local/bin/freebayes [21:24:08] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:24:08] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:24:08] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:24:08] Found vcfuniq - /usr/local/bin/vcfuniq [21:24:08] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:24:08] Found gzip - /bin/gzip [21:24:08] Found vt - /usr/local/bin/vt [21:24:08] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:24:08] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:24:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:24:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:24:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:24:09] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:24:09] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:24:09] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat [21:24:09] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat'
2[21:24:48] This is snippy 4.6.0
Show full stderr[21:24:48] This is snippy 4.6.0 [21:24:48] Written by Torsten Seemann [21:24:48] Obtained from https://github.com/tseemann/snippy [21:24:48] Detected operating system: linux [21:24:48] Enabling bundled linux tools. [21:24:48] Found bwa - /usr/local/bin/bwa [21:24:48] Found bcftools - /usr/local/bin/bcftools [21:24:48] Found samtools - /usr/local/bin/samtools [21:24:48] Found java - /usr/local/bin/java [21:24:48] Found snpEff - /usr/local/bin/snpEff [21:24:48] Found samclip - /usr/local/bin/samclip [21:24:48] Found seqtk - /usr/local/bin/seqtk [21:24:48] Found parallel - /usr/local/bin/parallel [21:24:48] Found freebayes - /usr/local/bin/freebayes [21:24:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:24:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:24:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:24:48] Found vcfuniq - /usr/local/bin/vcfuniq [21:24:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:24:48] Found gzip - /bin/gzip [21:24:48] Found vt - /usr/local/bin/vt [21:24:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:24:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:24:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:24:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:24:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:24:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:24:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:24:49] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat [21:24:49] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat'
2[21:24:50] This is snippy 4.6.0
Show full stderr[21:24:50] This is snippy 4.6.0 [21:24:50] Written by Torsten Seemann [21:24:50] Obtained from https://github.com/tseemann/snippy [21:24:50] Detected operating system: linux [21:24:50] Enabling bundled linux tools. [21:24:50] Found bwa - /usr/local/bin/bwa [21:24:50] Found bcftools - /usr/local/bin/bcftools [21:24:50] Found samtools - /usr/local/bin/samtools [21:24:50] Found java - /usr/local/bin/java [21:24:50] Found snpEff - /usr/local/bin/snpEff [21:24:50] Found samclip - /usr/local/bin/samclip [21:24:50] Found seqtk - /usr/local/bin/seqtk [21:24:50] Found parallel - /usr/local/bin/parallel [21:24:50] Found freebayes - /usr/local/bin/freebayes [21:24:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:24:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:24:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:24:50] Found vcfuniq - /usr/local/bin/vcfuniq [21:24:50] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:24:50] Found gzip - /bin/gzip [21:24:50] Found vt - /usr/local/bin/vt [21:24:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:24:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:24:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:24:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:24:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:24:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:24:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:24:51] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat [21:24:52] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat'
2[21:24:57] This is snippy 4.6.0
Show full stderr[21:24:57] This is snippy 4.6.0 [21:24:57] Written by Torsten Seemann [21:24:57] Obtained from https://github.com/tseemann/snippy [21:24:57] Detected operating system: linux [21:24:57] Enabling bundled linux tools. [21:24:57] Found bwa - /usr/local/bin/bwa [21:24:57] Found bcftools - /usr/local/bin/bcftools [21:24:57] Found samtools - /usr/local/bin/samtools [21:24:57] Found java - /usr/local/bin/java [21:24:57] Found snpEff - /usr/local/bin/snpEff [21:24:57] Found samclip - /usr/local/bin/samclip [21:24:57] Found seqtk - /usr/local/bin/seqtk [21:24:57] Found parallel - /usr/local/bin/parallel [21:24:57] Found freebayes - /usr/local/bin/freebayes [21:24:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:24:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:24:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:24:57] Found vcfuniq - /usr/local/bin/vcfuniq [21:24:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:24:57] Found gzip - /bin/gzip [21:24:57] Found vt - /usr/local/bin/vt [21:24:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:24:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:24:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:24:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:24:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:24:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:24:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:24:58] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat [21:24:58] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat'
2[21:25:15] This is snippy 4.6.0
Show full stderr[21:25:15] This is snippy 4.6.0 [21:25:15] Written by Torsten Seemann [21:25:15] Obtained from https://github.com/tseemann/snippy [21:25:15] Detected operating system: linux [21:25:15] Enabling bundled linux tools. [21:25:15] Found bwa - /usr/local/bin/bwa [21:25:15] Found bcftools - /usr/local/bin/bcftools [21:25:15] Found samtools - /usr/local/bin/samtools [21:25:15] Found java - /usr/local/bin/java [21:25:15] Found snpEff - /usr/local/bin/snpEff [21:25:15] Found samclip - /usr/local/bin/samclip [21:25:15] Found seqtk - /usr/local/bin/seqtk [21:25:15] Found parallel - /usr/local/bin/parallel [21:25:15] Found freebayes - /usr/local/bin/freebayes [21:25:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:25:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:25:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:25:15] Found vcfuniq - /usr/local/bin/vcfuniq [21:25:15] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:25:15] Found gzip - /bin/gzip [21:25:15] Found vt - /usr/local/bin/vt [21:25:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:25:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:25:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:25:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:25:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:25:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:25:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:25:16] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat [21:25:16] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat'
2[21:34:12] This is snippy 4.6.0
Show full stderr[21:34:12] This is snippy 4.6.0 [21:34:12] Written by Torsten Seemann [21:34:12] Obtained from https://github.com/tseemann/snippy [21:34:12] Detected operating system: linux [21:34:12] Enabling bundled linux tools. [21:34:12] Found bwa - /usr/local/bin/bwa [21:34:12] Found bcftools - /usr/local/bin/bcftools [21:34:12] Found samtools - /usr/local/bin/samtools [21:34:12] Found java - /usr/local/bin/java [21:34:12] Found snpEff - /usr/local/bin/snpEff [21:34:12] Found samclip - /usr/local/bin/samclip [21:34:12] Found seqtk - /usr/local/bin/seqtk [21:34:12] Found parallel - /usr/local/bin/parallel [21:34:12] Found freebayes - /usr/local/bin/freebayes [21:34:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:34:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:34:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:34:12] Found vcfuniq - /usr/local/bin/vcfuniq [21:34:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:34:12] Found gzip - /bin/gzip [21:34:12] Found vt - /usr/local/bin/vt [21:34:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:34:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:34:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:34:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:34:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:34:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:34:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:34:13] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat [21:34:13] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat'
2[21:34:42] This is snippy 4.6.0
Show full stderr[21:34:42] This is snippy 4.6.0 [21:34:42] Written by Torsten Seemann [21:34:42] Obtained from https://github.com/tseemann/snippy [21:34:42] Detected operating system: linux [21:34:42] Enabling bundled linux tools. [21:34:42] Found bwa - /usr/local/bin/bwa [21:34:42] Found bcftools - /usr/local/bin/bcftools [21:34:42] Found samtools - /usr/local/bin/samtools [21:34:42] Found java - /usr/local/bin/java [21:34:42] Found snpEff - /usr/local/bin/snpEff [21:34:42] Found samclip - /usr/local/bin/samclip [21:34:42] Found seqtk - /usr/local/bin/seqtk [21:34:42] Found parallel - /usr/local/bin/parallel [21:34:42] Found freebayes - /usr/local/bin/freebayes [21:34:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:34:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:34:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:34:42] Found vcfuniq - /usr/local/bin/vcfuniq [21:34:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:34:42] Found gzip - /bin/gzip [21:34:42] Found vt - /usr/local/bin/vt [21:34:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:34:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:34:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:34:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:34:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:34:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:34:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:34:43] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat [21:34:43] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat'
2[21:35:05] This is snippy 4.6.0
Show full stderr[21:35:05] This is snippy 4.6.0 [21:35:05] Written by Torsten Seemann [21:35:05] Obtained from https://github.com/tseemann/snippy [21:35:05] Detected operating system: linux [21:35:05] Enabling bundled linux tools. [21:35:05] Found bwa - /usr/local/bin/bwa [21:35:05] Found bcftools - /usr/local/bin/bcftools [21:35:05] Found samtools - /usr/local/bin/samtools [21:35:05] Found java - /usr/local/bin/java [21:35:05] Found snpEff - /usr/local/bin/snpEff [21:35:05] Found samclip - /usr/local/bin/samclip [21:35:05] Found seqtk - /usr/local/bin/seqtk [21:35:05] Found parallel - /usr/local/bin/parallel [21:35:05] Found freebayes - /usr/local/bin/freebayes [21:35:05] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:35:05] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:35:05] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:35:05] Found vcfuniq - /usr/local/bin/vcfuniq [21:35:05] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:35:05] Found gzip - /bin/gzip [21:35:05] Found vt - /usr/local/bin/vt [21:35:05] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:35:05] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:35:05] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:35:05] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:35:05] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:35:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:35:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:35:06] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat [21:35:06] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat'
2[21:35:29] This is snippy 4.6.0
Show full stderr[21:35:29] This is snippy 4.6.0 [21:35:29] Written by Torsten Seemann [21:35:29] Obtained from https://github.com/tseemann/snippy [21:35:29] Detected operating system: linux [21:35:29] Enabling bundled linux tools. [21:35:29] Found bwa - /usr/local/bin/bwa [21:35:29] Found bcftools - /usr/local/bin/bcftools [21:35:29] Found samtools - /usr/local/bin/samtools [21:35:29] Found java - /usr/local/bin/java [21:35:29] Found snpEff - /usr/local/bin/snpEff [21:35:29] Found samclip - /usr/local/bin/samclip [21:35:29] Found seqtk - /usr/local/bin/seqtk [21:35:29] Found parallel - /usr/local/bin/parallel [21:35:29] Found freebayes - /usr/local/bin/freebayes [21:35:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:35:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:35:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:35:29] Found vcfuniq - /usr/local/bin/vcfuniq [21:35:29] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:35:29] Found gzip - /bin/gzip [21:35:29] Found vt - /usr/local/bin/vt [21:35:29] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:35:29] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:35:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:35:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:35:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:35:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:35:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:35:31] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat [21:35:31] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat'
2[04:36:43] This is snippy 4.6.0
Show full stderr[04:36:43] This is snippy 4.6.0 [04:36:43] Written by Torsten Seemann [04:36:43] Obtained from https://github.com/tseemann/snippy [04:36:43] Detected operating system: linux [04:36:43] Enabling bundled linux tools. [04:36:43] Found bwa - /usr/local/bin/bwa [04:36:43] Found bcftools - /usr/local/bin/bcftools [04:36:43] Found samtools - /usr/local/bin/samtools [04:36:43] Found java - /usr/local/bin/java [04:36:43] Found snpEff - /usr/local/bin/snpEff [04:36:43] Found samclip - /usr/local/bin/samclip [04:36:43] Found seqtk - /usr/local/bin/seqtk [04:36:43] Found parallel - /usr/local/bin/parallel [04:36:43] Found freebayes - /usr/local/bin/freebayes [04:36:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:36:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:36:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:36:43] Found vcfuniq - /usr/local/bin/vcfuniq [04:36:43] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:36:43] Found gzip - /bin/gzip [04:36:43] Found vt - /usr/local/bin/vt [04:36:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:36:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:36:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:36:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:36:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:36:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:36:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:36:44] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:37:39] This is snippy 4.6.0
Show full stderr[04:37:39] This is snippy 4.6.0 [04:37:39] Written by Torsten Seemann [04:37:39] Obtained from https://github.com/tseemann/snippy [04:37:39] Detected operating system: linux [04:37:39] Enabling bundled linux tools. [04:37:39] Found bwa - /usr/local/bin/bwa [04:37:39] Found bcftools - /usr/local/bin/bcftools [04:37:39] Found samtools - /usr/local/bin/samtools [04:37:39] Found java - /usr/local/bin/java [04:37:39] Found snpEff - /usr/local/bin/snpEff [04:37:39] Found samclip - /usr/local/bin/samclip [04:37:39] Found seqtk - /usr/local/bin/seqtk [04:37:39] Found parallel - /usr/local/bin/parallel [04:37:39] Found freebayes - /usr/local/bin/freebayes [04:37:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:37:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:37:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:37:39] Found vcfuniq - /usr/local/bin/vcfuniq [04:37:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:37:39] Found gzip - /bin/gzip [04:37:39] Found vt - /usr/local/bin/vt [04:37:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:37:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:37:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:37:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:37:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:37:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:37:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:37:40] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:38:30] This is snippy 4.6.0
Show full stderr[04:38:30] This is snippy 4.6.0 [04:38:30] Written by Torsten Seemann [04:38:30] Obtained from https://github.com/tseemann/snippy [04:38:30] Detected operating system: linux [04:38:30] Enabling bundled linux tools. [04:38:30] Found bwa - /usr/local/bin/bwa [04:38:30] Found bcftools - /usr/local/bin/bcftools [04:38:30] Found samtools - /usr/local/bin/samtools [04:38:30] Found java - /usr/local/bin/java [04:38:30] Found snpEff - /usr/local/bin/snpEff [04:38:30] Found samclip - /usr/local/bin/samclip [04:38:30] Found seqtk - /usr/local/bin/seqtk [04:38:30] Found parallel - /usr/local/bin/parallel [04:38:30] Found freebayes - /usr/local/bin/freebayes [04:38:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:38:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:38:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:38:30] Found vcfuniq - /usr/local/bin/vcfuniq [04:38:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:38:30] Found gzip - /bin/gzip [04:38:30] Found vt - /usr/local/bin/vt [04:38:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:38:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:38:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:38:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:38:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:38:30] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:38:30] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:38:30] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:38:36] This is snippy 4.6.0
Show full stderr[04:38:36] This is snippy 4.6.0 [04:38:36] Written by Torsten Seemann [04:38:36] Obtained from https://github.com/tseemann/snippy [04:38:36] Detected operating system: linux [04:38:36] Enabling bundled linux tools. [04:38:36] Found bwa - /usr/local/bin/bwa [04:38:36] Found bcftools - /usr/local/bin/bcftools [04:38:36] Found samtools - /usr/local/bin/samtools [04:38:36] Found java - /usr/local/bin/java [04:38:36] Found snpEff - /usr/local/bin/snpEff [04:38:36] Found samclip - /usr/local/bin/samclip [04:38:36] Found seqtk - /usr/local/bin/seqtk [04:38:36] Found parallel - /usr/local/bin/parallel [04:38:36] Found freebayes - /usr/local/bin/freebayes [04:38:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:38:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:38:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:38:36] Found vcfuniq - /usr/local/bin/vcfuniq [04:38:36] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:38:36] Found gzip - /bin/gzip [04:38:36] Found vt - /usr/local/bin/vt [04:38:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:38:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:38:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:38:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:38:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:38:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:38:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:38:36] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:38:06] This is snippy 4.6.0
Show full stderr[04:38:06] This is snippy 4.6.0 [04:38:06] Written by Torsten Seemann [04:38:06] Obtained from https://github.com/tseemann/snippy [04:38:06] Detected operating system: linux [04:38:06] Enabling bundled linux tools. [04:38:06] Found bwa - /usr/local/bin/bwa [04:38:06] Found bcftools - /usr/local/bin/bcftools [04:38:06] Found samtools - /usr/local/bin/samtools [04:38:06] Found java - /usr/local/bin/java [04:38:06] Found snpEff - /usr/local/bin/snpEff [04:38:06] Found samclip - /usr/local/bin/samclip [04:38:06] Found seqtk - /usr/local/bin/seqtk [04:38:06] Found parallel - /usr/local/bin/parallel [04:38:06] Found freebayes - /usr/local/bin/freebayes [04:38:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:38:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:38:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:38:06] Found vcfuniq - /usr/local/bin/vcfuniq [04:38:06] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:38:06] Found gzip - /bin/gzip [04:38:06] Found vt - /usr/local/bin/vt [04:38:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:38:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:38:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:38:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:38:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:38:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:38:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:38:07] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:38:54] This is snippy 4.6.0
Show full stderr[04:38:54] This is snippy 4.6.0 [04:38:54] Written by Torsten Seemann [04:38:54] Obtained from https://github.com/tseemann/snippy [04:38:54] Detected operating system: linux [04:38:54] Enabling bundled linux tools. [04:38:54] Found bwa - /usr/local/bin/bwa [04:38:54] Found bcftools - /usr/local/bin/bcftools [04:38:54] Found samtools - /usr/local/bin/samtools [04:38:54] Found java - /usr/local/bin/java [04:38:54] Found snpEff - /usr/local/bin/snpEff [04:38:54] Found samclip - /usr/local/bin/samclip [04:38:54] Found seqtk - /usr/local/bin/seqtk [04:38:54] Found parallel - /usr/local/bin/parallel [04:38:54] Found freebayes - /usr/local/bin/freebayes [04:38:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:38:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:38:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:38:54] Found vcfuniq - /usr/local/bin/vcfuniq [04:38:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:38:54] Found gzip - /bin/gzip [04:38:54] Found vt - /usr/local/bin/vt [04:38:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:38:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:38:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:38:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:38:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:38:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:38:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:38:54] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:40:06] This is snippy 4.6.0
Show full stderr[04:40:06] This is snippy 4.6.0 [04:40:06] Written by Torsten Seemann [04:40:06] Obtained from https://github.com/tseemann/snippy [04:40:06] Detected operating system: linux [04:40:06] Enabling bundled linux tools. [04:40:06] Found bwa - /usr/local/bin/bwa [04:40:06] Found bcftools - /usr/local/bin/bcftools [04:40:06] Found samtools - /usr/local/bin/samtools [04:40:06] Found java - /usr/local/bin/java [04:40:06] Found snpEff - /usr/local/bin/snpEff [04:40:06] Found samclip - /usr/local/bin/samclip [04:40:06] Found seqtk - /usr/local/bin/seqtk [04:40:06] Found parallel - /usr/local/bin/parallel [04:40:06] Found freebayes - /usr/local/bin/freebayes [04:40:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:40:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:40:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:40:06] Found vcfuniq - /usr/local/bin/vcfuniq [04:40:06] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:40:06] Found gzip - /bin/gzip [04:40:06] Found vt - /usr/local/bin/vt [04:40:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:40:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:40:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:40:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:40:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:40:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:40:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:40:07] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:37:42] This is snippy 4.6.0
Show full stderr[04:37:42] This is snippy 4.6.0 [04:37:42] Written by Torsten Seemann [04:37:42] Obtained from https://github.com/tseemann/snippy [04:37:42] Detected operating system: linux [04:37:42] Enabling bundled linux tools. [04:37:42] Found bwa - /usr/local/bin/bwa [04:37:42] Found bcftools - /usr/local/bin/bcftools [04:37:42] Found samtools - /usr/local/bin/samtools [04:37:42] Found java - /usr/local/bin/java [04:37:42] Found snpEff - /usr/local/bin/snpEff [04:37:42] Found samclip - /usr/local/bin/samclip [04:37:42] Found seqtk - /usr/local/bin/seqtk [04:37:42] Found parallel - /usr/local/bin/parallel [04:37:42] Found freebayes - /usr/local/bin/freebayes [04:37:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:37:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:37:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:37:42] Found vcfuniq - /usr/local/bin/vcfuniq [04:37:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:37:42] Found gzip - /bin/gzip [04:37:42] Found vt - /usr/local/bin/vt [04:37:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:37:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:37:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:37:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:37:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:37:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:37:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:37:43] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:38:12] This is snippy 4.6.0
Show full stderr[04:38:12] This is snippy 4.6.0 [04:38:12] Written by Torsten Seemann [04:38:12] Obtained from https://github.com/tseemann/snippy [04:38:12] Detected operating system: linux [04:38:12] Enabling bundled linux tools. [04:38:12] Found bwa - /usr/local/bin/bwa [04:38:12] Found bcftools - /usr/local/bin/bcftools [04:38:12] Found samtools - /usr/local/bin/samtools [04:38:12] Found java - /usr/local/bin/java [04:38:12] Found snpEff - /usr/local/bin/snpEff [04:38:12] Found samclip - /usr/local/bin/samclip [04:38:12] Found seqtk - /usr/local/bin/seqtk [04:38:12] Found parallel - /usr/local/bin/parallel [04:38:12] Found freebayes - /usr/local/bin/freebayes [04:38:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:38:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:38:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:38:12] Found vcfuniq - /usr/local/bin/vcfuniq [04:38:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:38:12] Found gzip - /bin/gzip [04:38:12] Found vt - /usr/local/bin/vt [04:38:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:38:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:38:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:38:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:38:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:38:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:38:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:38:13] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:38:51] This is snippy 4.6.0
Show full stderr[04:38:51] This is snippy 4.6.0 [04:38:51] Written by Torsten Seemann [04:38:51] Obtained from https://github.com/tseemann/snippy [04:38:51] Detected operating system: linux [04:38:51] Enabling bundled linux tools. [04:38:51] Found bwa - /usr/local/bin/bwa [04:38:51] Found bcftools - /usr/local/bin/bcftools [04:38:51] Found samtools - /usr/local/bin/samtools [04:38:51] Found java - /usr/local/bin/java [04:38:51] Found snpEff - /usr/local/bin/snpEff [04:38:51] Found samclip - /usr/local/bin/samclip [04:38:51] Found seqtk - /usr/local/bin/seqtk [04:38:51] Found parallel - /usr/local/bin/parallel [04:38:51] Found freebayes - /usr/local/bin/freebayes [04:38:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:38:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:38:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:38:51] Found vcfuniq - /usr/local/bin/vcfuniq [04:38:51] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:38:51] Found gzip - /bin/gzip [04:38:51] Found vt - /usr/local/bin/vt [04:38:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:38:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:38:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:38:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:38:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:38:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:38:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:38:52] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:39:06] This is snippy 4.6.0
Show full stderr[04:39:06] This is snippy 4.6.0 [04:39:06] Written by Torsten Seemann [04:39:06] Obtained from https://github.com/tseemann/snippy [04:39:06] Detected operating system: linux [04:39:06] Enabling bundled linux tools. [04:39:06] Found bwa - /usr/local/bin/bwa [04:39:06] Found bcftools - /usr/local/bin/bcftools [04:39:06] Found samtools - /usr/local/bin/samtools [04:39:06] Found java - /usr/local/bin/java [04:39:06] Found snpEff - /usr/local/bin/snpEff [04:39:06] Found samclip - /usr/local/bin/samclip [04:39:06] Found seqtk - /usr/local/bin/seqtk [04:39:06] Found parallel - /usr/local/bin/parallel [04:39:06] Found freebayes - /usr/local/bin/freebayes [04:39:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:39:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:39:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:39:06] Found vcfuniq - /usr/local/bin/vcfuniq [04:39:06] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:39:06] Found gzip - /bin/gzip [04:39:06] Found vt - /usr/local/bin/vt [04:39:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:39:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:39:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:39:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:39:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:39:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:39:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:39:07] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:40:12] This is snippy 4.6.0
Show full stderr[04:40:12] This is snippy 4.6.0 [04:40:12] Written by Torsten Seemann [04:40:12] Obtained from https://github.com/tseemann/snippy [04:40:12] Detected operating system: linux [04:40:12] Enabling bundled linux tools. [04:40:12] Found bwa - /usr/local/bin/bwa [04:40:12] Found bcftools - /usr/local/bin/bcftools [04:40:12] Found samtools - /usr/local/bin/samtools [04:40:12] Found java - /usr/local/bin/java [04:40:12] Found snpEff - /usr/local/bin/snpEff [04:40:12] Found samclip - /usr/local/bin/samclip [04:40:12] Found seqtk - /usr/local/bin/seqtk [04:40:12] Found parallel - /usr/local/bin/parallel [04:40:12] Found freebayes - /usr/local/bin/freebayes [04:40:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:40:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:40:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:40:12] Found vcfuniq - /usr/local/bin/vcfuniq [04:40:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:40:12] Found gzip - /bin/gzip [04:40:12] Found vt - /usr/local/bin/vt [04:40:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:40:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:40:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:40:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:40:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:40:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:40:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:40:13] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:39:36] This is snippy 4.6.0
Show full stderr[04:39:36] This is snippy 4.6.0 [04:39:36] Written by Torsten Seemann [04:39:36] Obtained from https://github.com/tseemann/snippy [04:39:36] Detected operating system: linux [04:39:36] Enabling bundled linux tools. [04:39:36] Found bwa - /usr/local/bin/bwa [04:39:36] Found bcftools - /usr/local/bin/bcftools [04:39:36] Found samtools - /usr/local/bin/samtools [04:39:36] Found java - /usr/local/bin/java [04:39:36] Found snpEff - /usr/local/bin/snpEff [04:39:36] Found samclip - /usr/local/bin/samclip [04:39:36] Found seqtk - /usr/local/bin/seqtk [04:39:36] Found parallel - /usr/local/bin/parallel [04:39:36] Found freebayes - /usr/local/bin/freebayes [04:39:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:39:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:39:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:39:36] Found vcfuniq - /usr/local/bin/vcfuniq [04:39:36] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:39:36] Found gzip - /bin/gzip [04:39:36] Found vt - /usr/local/bin/vt [04:39:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:39:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:39:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:39:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:39:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:39:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:39:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:39:37] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:39:51] This is snippy 4.6.0
Show full stderr[04:39:51] This is snippy 4.6.0 [04:39:51] Written by Torsten Seemann [04:39:51] Obtained from https://github.com/tseemann/snippy [04:39:51] Detected operating system: linux [04:39:51] Enabling bundled linux tools. [04:39:51] Found bwa - /usr/local/bin/bwa [04:39:51] Found bcftools - /usr/local/bin/bcftools [04:39:51] Found samtools - /usr/local/bin/samtools [04:39:51] Found java - /usr/local/bin/java [04:39:51] Found snpEff - /usr/local/bin/snpEff [04:39:51] Found samclip - /usr/local/bin/samclip [04:39:51] Found seqtk - /usr/local/bin/seqtk [04:39:51] Found parallel - /usr/local/bin/parallel [04:39:51] Found freebayes - /usr/local/bin/freebayes [04:39:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:39:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:39:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:39:51] Found vcfuniq - /usr/local/bin/vcfuniq [04:39:51] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:39:51] Found gzip - /bin/gzip [04:39:51] Found vt - /usr/local/bin/vt [04:39:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:39:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:39:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:39:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:39:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:39:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:39:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:39:52] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:40:15] This is snippy 4.6.0
Show full stderr[04:40:15] This is snippy 4.6.0 [04:40:15] Written by Torsten Seemann [04:40:15] Obtained from https://github.com/tseemann/snippy [04:40:15] Detected operating system: linux [04:40:15] Enabling bundled linux tools. [04:40:15] Found bwa - /usr/local/bin/bwa [04:40:15] Found bcftools - /usr/local/bin/bcftools [04:40:15] Found samtools - /usr/local/bin/samtools [04:40:15] Found java - /usr/local/bin/java [04:40:15] Found snpEff - /usr/local/bin/snpEff [04:40:15] Found samclip - /usr/local/bin/samclip [04:40:15] Found seqtk - /usr/local/bin/seqtk [04:40:15] Found parallel - /usr/local/bin/parallel [04:40:15] Found freebayes - /usr/local/bin/freebayes [04:40:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:40:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:40:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:40:15] Found vcfuniq - /usr/local/bin/vcfuniq [04:40:15] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:40:15] Found gzip - /bin/gzip [04:40:15] Found vt - /usr/local/bin/vt [04:40:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:40:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:40:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:40:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:40:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:40:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:40:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:40:16] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:40:21] This is snippy 4.6.0
Show full stderr[04:40:21] This is snippy 4.6.0 [04:40:21] Written by Torsten Seemann [04:40:21] Obtained from https://github.com/tseemann/snippy [04:40:21] Detected operating system: linux [04:40:21] Enabling bundled linux tools. [04:40:21] Found bwa - /usr/local/bin/bwa [04:40:21] Found bcftools - /usr/local/bin/bcftools [04:40:21] Found samtools - /usr/local/bin/samtools [04:40:21] Found java - /usr/local/bin/java [04:40:21] Found snpEff - /usr/local/bin/snpEff [04:40:21] Found samclip - /usr/local/bin/samclip [04:40:21] Found seqtk - /usr/local/bin/seqtk [04:40:21] Found parallel - /usr/local/bin/parallel [04:40:21] Found freebayes - /usr/local/bin/freebayes [04:40:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:40:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:40:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:40:21] Found vcfuniq - /usr/local/bin/vcfuniq [04:40:21] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:40:21] Found gzip - /bin/gzip [04:40:21] Found vt - /usr/local/bin/vt [04:40:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:40:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:40:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:40:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:40:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:40:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:40:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:40:22] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:41:21] This is snippy 4.6.0
Show full stderr[04:41:21] This is snippy 4.6.0 [04:41:21] Written by Torsten Seemann [04:41:21] Obtained from https://github.com/tseemann/snippy [04:41:21] Detected operating system: linux [04:41:21] Enabling bundled linux tools. [04:41:21] Found bwa - /usr/local/bin/bwa [04:41:21] Found bcftools - /usr/local/bin/bcftools [04:41:21] Found samtools - /usr/local/bin/samtools [04:41:21] Found java - /usr/local/bin/java [04:41:21] Found snpEff - /usr/local/bin/snpEff [04:41:21] Found samclip - /usr/local/bin/samclip [04:41:21] Found seqtk - /usr/local/bin/seqtk [04:41:21] Found parallel - /usr/local/bin/parallel [04:41:21] Found freebayes - /usr/local/bin/freebayes [04:41:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:41:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:41:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:41:21] Found vcfuniq - /usr/local/bin/vcfuniq [04:41:21] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:41:21] Found gzip - /bin/gzip [04:41:21] Found vt - /usr/local/bin/vt [04:41:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:41:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:41:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:41:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:41:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:41:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:41:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:41:22] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:42:00] This is snippy 4.6.0
Show full stderr[04:42:00] This is snippy 4.6.0 [04:42:00] Written by Torsten Seemann [04:42:00] Obtained from https://github.com/tseemann/snippy [04:42:00] Detected operating system: linux [04:42:00] Enabling bundled linux tools. [04:42:00] Found bwa - /usr/local/bin/bwa [04:42:00] Found bcftools - /usr/local/bin/bcftools [04:42:00] Found samtools - /usr/local/bin/samtools [04:42:00] Found java - /usr/local/bin/java [04:42:00] Found snpEff - /usr/local/bin/snpEff [04:42:00] Found samclip - /usr/local/bin/samclip [04:42:00] Found seqtk - /usr/local/bin/seqtk [04:42:00] Found parallel - /usr/local/bin/parallel [04:42:00] Found freebayes - /usr/local/bin/freebayes [04:42:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:42:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:42:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:42:00] Found vcfuniq - /usr/local/bin/vcfuniq [04:42:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:42:00] Found gzip - /bin/gzip [04:42:00] Found vt - /usr/local/bin/vt [04:42:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:42:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:42:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:42:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:42:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:42:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:42:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:42:01] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:41:34] This is snippy 4.6.0
Show full stderr[04:41:34] This is snippy 4.6.0 [04:41:34] Written by Torsten Seemann [04:41:34] Obtained from https://github.com/tseemann/snippy [04:41:34] Detected operating system: linux [04:41:34] Enabling bundled linux tools. [04:41:34] Found bwa - /usr/local/bin/bwa [04:41:34] Found bcftools - /usr/local/bin/bcftools [04:41:34] Found samtools - /usr/local/bin/samtools [04:41:34] Found java - /usr/local/bin/java [04:41:34] Found snpEff - /usr/local/bin/snpEff [04:41:34] Found samclip - /usr/local/bin/samclip [04:41:34] Found seqtk - /usr/local/bin/seqtk [04:41:34] Found parallel - /usr/local/bin/parallel [04:41:34] Found freebayes - /usr/local/bin/freebayes [04:41:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:41:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:41:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:41:34] Found vcfuniq - /usr/local/bin/vcfuniq [04:41:34] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:41:34] Found gzip - /bin/gzip [04:41:34] Found vt - /usr/local/bin/vt [04:41:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:41:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:41:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:41:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:41:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:41:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:41:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:41:35] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:41:49] This is snippy 4.6.0
Show full stderr[04:41:49] This is snippy 4.6.0 [04:41:49] Written by Torsten Seemann [04:41:49] Obtained from https://github.com/tseemann/snippy [04:41:49] Detected operating system: linux [04:41:49] Enabling bundled linux tools. [04:41:49] Found bwa - /usr/local/bin/bwa [04:41:49] Found bcftools - /usr/local/bin/bcftools [04:41:49] Found samtools - /usr/local/bin/samtools [04:41:49] Found java - /usr/local/bin/java [04:41:49] Found snpEff - /usr/local/bin/snpEff [04:41:49] Found samclip - /usr/local/bin/samclip [04:41:49] Found seqtk - /usr/local/bin/seqtk [04:41:49] Found parallel - /usr/local/bin/parallel [04:41:49] Found freebayes - /usr/local/bin/freebayes [04:41:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:41:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:41:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:41:49] Found vcfuniq - /usr/local/bin/vcfuniq [04:41:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:41:49] Found gzip - /bin/gzip [04:41:49] Found vt - /usr/local/bin/vt [04:41:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:41:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:41:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:41:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:41:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:41:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:41:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:41:50] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:42:06] This is snippy 4.6.0
Show full stderr[04:42:06] This is snippy 4.6.0 [04:42:06] Written by Torsten Seemann [04:42:06] Obtained from https://github.com/tseemann/snippy [04:42:06] Detected operating system: linux [04:42:06] Enabling bundled linux tools. [04:42:06] Found bwa - /usr/local/bin/bwa [04:42:06] Found bcftools - /usr/local/bin/bcftools [04:42:06] Found samtools - /usr/local/bin/samtools [04:42:06] Found java - /usr/local/bin/java [04:42:06] Found snpEff - /usr/local/bin/snpEff [04:42:06] Found samclip - /usr/local/bin/samclip [04:42:06] Found seqtk - /usr/local/bin/seqtk [04:42:06] Found parallel - /usr/local/bin/parallel [04:42:06] Found freebayes - /usr/local/bin/freebayes [04:42:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:42:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:42:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:42:06] Found vcfuniq - /usr/local/bin/vcfuniq [04:42:06] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:42:06] Found gzip - /bin/gzip [04:42:06] Found vt - /usr/local/bin/vt [04:42:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:42:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:42:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:42:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:42:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:42:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:42:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:42:07] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:42:33] This is snippy 4.6.0
Show full stderr[04:42:33] This is snippy 4.6.0 [04:42:33] Written by Torsten Seemann [04:42:33] Obtained from https://github.com/tseemann/snippy [04:42:33] Detected operating system: linux [04:42:33] Enabling bundled linux tools. [04:42:33] Found bwa - /usr/local/bin/bwa [04:42:33] Found bcftools - /usr/local/bin/bcftools [04:42:33] Found samtools - /usr/local/bin/samtools [04:42:33] Found java - /usr/local/bin/java [04:42:33] Found snpEff - /usr/local/bin/snpEff [04:42:33] Found samclip - /usr/local/bin/samclip [04:42:33] Found seqtk - /usr/local/bin/seqtk [04:42:33] Found parallel - /usr/local/bin/parallel [04:42:33] Found freebayes - /usr/local/bin/freebayes [04:42:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:42:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:42:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:42:33] Found vcfuniq - /usr/local/bin/vcfuniq [04:42:33] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:42:33] Found gzip - /bin/gzip [04:42:33] Found vt - /usr/local/bin/vt [04:42:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:42:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:42:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:42:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:42:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:42:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:42:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:42:34] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:40:32] This is snippy 4.6.0
Show full stderr[04:40:32] This is snippy 4.6.0 [04:40:32] Written by Torsten Seemann [04:40:32] Obtained from https://github.com/tseemann/snippy [04:40:32] Detected operating system: linux [04:40:32] Enabling bundled linux tools. [04:40:32] Found bwa - /usr/local/bin/bwa [04:40:32] Found bcftools - /usr/local/bin/bcftools [04:40:32] Found samtools - /usr/local/bin/samtools [04:40:32] Found java - /usr/local/bin/java [04:40:32] Found snpEff - /usr/local/bin/snpEff [04:40:32] Found samclip - /usr/local/bin/samclip [04:40:32] Found seqtk - /usr/local/bin/seqtk [04:40:32] Found parallel - /usr/local/bin/parallel [04:40:32] Found freebayes - /usr/local/bin/freebayes [04:40:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:40:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:40:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:40:32] Found vcfuniq - /usr/local/bin/vcfuniq [04:40:32] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:40:32] Found gzip - /bin/gzip [04:40:32] Found vt - /usr/local/bin/vt [04:40:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:40:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:40:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:40:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:40:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:40:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:40:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:40:33] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:40:50] This is snippy 4.6.0
Show full stderr[04:40:50] This is snippy 4.6.0 [04:40:50] Written by Torsten Seemann [04:40:50] Obtained from https://github.com/tseemann/snippy [04:40:50] Detected operating system: linux [04:40:50] Enabling bundled linux tools. [04:40:50] Found bwa - /usr/local/bin/bwa [04:40:50] Found bcftools - /usr/local/bin/bcftools [04:40:50] Found samtools - /usr/local/bin/samtools [04:40:50] Found java - /usr/local/bin/java [04:40:50] Found snpEff - /usr/local/bin/snpEff [04:40:50] Found samclip - /usr/local/bin/samclip [04:40:50] Found seqtk - /usr/local/bin/seqtk [04:40:50] Found parallel - /usr/local/bin/parallel [04:40:50] Found freebayes - /usr/local/bin/freebayes [04:40:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:40:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:40:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:40:50] Found vcfuniq - /usr/local/bin/vcfuniq [04:40:50] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:40:50] Found gzip - /bin/gzip [04:40:50] Found vt - /usr/local/bin/vt [04:40:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:40:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:40:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:40:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:40:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:40:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:40:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:40:51] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:41:37] This is snippy 4.6.0
Show full stderr[04:41:37] This is snippy 4.6.0 [04:41:37] Written by Torsten Seemann [04:41:37] Obtained from https://github.com/tseemann/snippy [04:41:37] Detected operating system: linux [04:41:37] Enabling bundled linux tools. [04:41:37] Found bwa - /usr/local/bin/bwa [04:41:37] Found bcftools - /usr/local/bin/bcftools [04:41:37] Found samtools - /usr/local/bin/samtools [04:41:37] Found java - /usr/local/bin/java [04:41:37] Found snpEff - /usr/local/bin/snpEff [04:41:37] Found samclip - /usr/local/bin/samclip [04:41:37] Found seqtk - /usr/local/bin/seqtk [04:41:37] Found parallel - /usr/local/bin/parallel [04:41:37] Found freebayes - /usr/local/bin/freebayes [04:41:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:41:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:41:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:41:37] Found vcfuniq - /usr/local/bin/vcfuniq [04:41:37] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:41:37] Found gzip - /bin/gzip [04:41:37] Found vt - /usr/local/bin/vt [04:41:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:41:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:41:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:41:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:41:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:41:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:41:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:41:38] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:42:03] This is snippy 4.6.0
Show full stderr[04:42:03] This is snippy 4.6.0 [04:42:03] Written by Torsten Seemann [04:42:03] Obtained from https://github.com/tseemann/snippy [04:42:03] Detected operating system: linux [04:42:03] Enabling bundled linux tools. [04:42:03] Found bwa - /usr/local/bin/bwa [04:42:03] Found bcftools - /usr/local/bin/bcftools [04:42:03] Found samtools - /usr/local/bin/samtools [04:42:03] Found java - /usr/local/bin/java [04:42:03] Found snpEff - /usr/local/bin/snpEff [04:42:03] Found samclip - /usr/local/bin/samclip [04:42:03] Found seqtk - /usr/local/bin/seqtk [04:42:03] Found parallel - /usr/local/bin/parallel [04:42:03] Found freebayes - /usr/local/bin/freebayes [04:42:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:42:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:42:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:42:03] Found vcfuniq - /usr/local/bin/vcfuniq [04:42:03] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:42:03] Found gzip - /bin/gzip [04:42:03] Found vt - /usr/local/bin/vt [04:42:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:42:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:42:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:42:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:42:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:42:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:42:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:42:04] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:42:57] This is snippy 4.6.0
Show full stderr[04:42:57] This is snippy 4.6.0 [04:42:57] Written by Torsten Seemann [04:42:57] Obtained from https://github.com/tseemann/snippy [04:42:57] Detected operating system: linux [04:42:57] Enabling bundled linux tools. [04:42:57] Found bwa - /usr/local/bin/bwa [04:42:57] Found bcftools - /usr/local/bin/bcftools [04:42:57] Found samtools - /usr/local/bin/samtools [04:42:57] Found java - /usr/local/bin/java [04:42:57] Found snpEff - /usr/local/bin/snpEff [04:42:57] Found samclip - /usr/local/bin/samclip [04:42:57] Found seqtk - /usr/local/bin/seqtk [04:42:57] Found parallel - /usr/local/bin/parallel [04:42:57] Found freebayes - /usr/local/bin/freebayes [04:42:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:42:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:42:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:42:57] Found vcfuniq - /usr/local/bin/vcfuniq [04:42:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:42:57] Found gzip - /bin/gzip [04:42:57] Found vt - /usr/local/bin/vt [04:42:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:42:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:42:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:42:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:42:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:42:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:42:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:42:58] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:43:09] This is snippy 4.6.0
Show full stderr[04:43:09] This is snippy 4.6.0 [04:43:09] Written by Torsten Seemann [04:43:09] Obtained from https://github.com/tseemann/snippy [04:43:09] Detected operating system: linux [04:43:09] Enabling bundled linux tools. [04:43:09] Found bwa - /usr/local/bin/bwa [04:43:09] Found bcftools - /usr/local/bin/bcftools [04:43:09] Found samtools - /usr/local/bin/samtools [04:43:09] Found java - /usr/local/bin/java [04:43:09] Found snpEff - /usr/local/bin/snpEff [04:43:09] Found samclip - /usr/local/bin/samclip [04:43:09] Found seqtk - /usr/local/bin/seqtk [04:43:09] Found parallel - /usr/local/bin/parallel [04:43:09] Found freebayes - /usr/local/bin/freebayes [04:43:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:43:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:43:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:43:09] Found vcfuniq - /usr/local/bin/vcfuniq [04:43:09] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:43:09] Found gzip - /bin/gzip [04:43:09] Found vt - /usr/local/bin/vt [04:43:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:43:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:43:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:43:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:43:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:43:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:43:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:43:10] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:43:49] This is snippy 4.6.0
Show full stderr[04:43:49] This is snippy 4.6.0 [04:43:49] Written by Torsten Seemann [04:43:49] Obtained from https://github.com/tseemann/snippy [04:43:49] Detected operating system: linux [04:43:49] Enabling bundled linux tools. [04:43:49] Found bwa - /usr/local/bin/bwa [04:43:49] Found bcftools - /usr/local/bin/bcftools [04:43:49] Found samtools - /usr/local/bin/samtools [04:43:49] Found java - /usr/local/bin/java [04:43:49] Found snpEff - /usr/local/bin/snpEff [04:43:49] Found samclip - /usr/local/bin/samclip [04:43:49] Found seqtk - /usr/local/bin/seqtk [04:43:49] Found parallel - /usr/local/bin/parallel [04:43:49] Found freebayes - /usr/local/bin/freebayes [04:43:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:43:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:43:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:43:49] Found vcfuniq - /usr/local/bin/vcfuniq [04:43:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:43:49] Found gzip - /bin/gzip [04:43:49] Found vt - /usr/local/bin/vt [04:43:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:43:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:43:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:43:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:43:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:43:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:43:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:43:50] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:44:01] This is snippy 4.6.0
Show full stderr[04:44:01] This is snippy 4.6.0 [04:44:01] Written by Torsten Seemann [04:44:01] Obtained from https://github.com/tseemann/snippy [04:44:01] Detected operating system: linux [04:44:01] Enabling bundled linux tools. [04:44:01] Found bwa - /usr/local/bin/bwa [04:44:01] Found bcftools - /usr/local/bin/bcftools [04:44:01] Found samtools - /usr/local/bin/samtools [04:44:01] Found java - /usr/local/bin/java [04:44:01] Found snpEff - /usr/local/bin/snpEff [04:44:01] Found samclip - /usr/local/bin/samclip [04:44:01] Found seqtk - /usr/local/bin/seqtk [04:44:01] Found parallel - /usr/local/bin/parallel [04:44:01] Found freebayes - /usr/local/bin/freebayes [04:44:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:44:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:44:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:44:01] Found vcfuniq - /usr/local/bin/vcfuniq [04:44:01] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:44:01] Found gzip - /bin/gzip [04:44:01] Found vt - /usr/local/bin/vt [04:44:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:44:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:44:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:44:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:44:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:44:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:44:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:44:02] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:44:10] This is snippy 4.6.0
Show full stderr[04:44:10] This is snippy 4.6.0 [04:44:10] Written by Torsten Seemann [04:44:10] Obtained from https://github.com/tseemann/snippy [04:44:10] Detected operating system: linux [04:44:10] Enabling bundled linux tools. [04:44:10] Found bwa - /usr/local/bin/bwa [04:44:10] Found bcftools - /usr/local/bin/bcftools [04:44:10] Found samtools - /usr/local/bin/samtools [04:44:10] Found java - /usr/local/bin/java [04:44:10] Found snpEff - /usr/local/bin/snpEff [04:44:10] Found samclip - /usr/local/bin/samclip [04:44:10] Found seqtk - /usr/local/bin/seqtk [04:44:10] Found parallel - /usr/local/bin/parallel [04:44:10] Found freebayes - /usr/local/bin/freebayes [04:44:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:44:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:44:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:44:10] Found vcfuniq - /usr/local/bin/vcfuniq [04:44:10] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:44:10] Found gzip - /bin/gzip [04:44:10] Found vt - /usr/local/bin/vt [04:44:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:44:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:44:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:44:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:44:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:44:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:44:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:44:11] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:44:31] This is snippy 4.6.0
Show full stderr[04:44:31] This is snippy 4.6.0 [04:44:31] Written by Torsten Seemann [04:44:31] Obtained from https://github.com/tseemann/snippy [04:44:31] Detected operating system: linux [04:44:31] Enabling bundled linux tools. [04:44:31] Found bwa - /usr/local/bin/bwa [04:44:31] Found bcftools - /usr/local/bin/bcftools [04:44:31] Found samtools - /usr/local/bin/samtools [04:44:31] Found java - /usr/local/bin/java [04:44:31] Found snpEff - /usr/local/bin/snpEff [04:44:31] Found samclip - /usr/local/bin/samclip [04:44:31] Found seqtk - /usr/local/bin/seqtk [04:44:32] Found parallel - /usr/local/bin/parallel [04:44:32] Found freebayes - /usr/local/bin/freebayes [04:44:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:44:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:44:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:44:32] Found vcfuniq - /usr/local/bin/vcfuniq [04:44:32] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:44:32] Found gzip - /bin/gzip [04:44:32] Found vt - /usr/local/bin/vt [04:44:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:44:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:44:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:44:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:44:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:44:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:44:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:44:33] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:44:13] This is snippy 4.6.0
Show full stderr[04:44:13] This is snippy 4.6.0 [04:44:13] Written by Torsten Seemann [04:44:13] Obtained from https://github.com/tseemann/snippy [04:44:13] Detected operating system: linux [04:44:13] Enabling bundled linux tools. [04:44:13] Found bwa - /usr/local/bin/bwa [04:44:13] Found bcftools - /usr/local/bin/bcftools [04:44:13] Found samtools - /usr/local/bin/samtools [04:44:13] Found java - /usr/local/bin/java [04:44:13] Found snpEff - /usr/local/bin/snpEff [04:44:13] Found samclip - /usr/local/bin/samclip [04:44:13] Found seqtk - /usr/local/bin/seqtk [04:44:13] Found parallel - /usr/local/bin/parallel [04:44:13] Found freebayes - /usr/local/bin/freebayes [04:44:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:44:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:44:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:44:13] Found vcfuniq - /usr/local/bin/vcfuniq [04:44:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:44:13] Found gzip - /bin/gzip [04:44:13] Found vt - /usr/local/bin/vt [04:44:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:44:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:44:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:44:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:44:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:44:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:44:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:44:14] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:44:25] This is snippy 4.6.0
Show full stderr[04:44:25] This is snippy 4.6.0 [04:44:25] Written by Torsten Seemann [04:44:25] Obtained from https://github.com/tseemann/snippy [04:44:25] Detected operating system: linux [04:44:25] Enabling bundled linux tools. [04:44:25] Found bwa - /usr/local/bin/bwa [04:44:25] Found bcftools - /usr/local/bin/bcftools [04:44:25] Found samtools - /usr/local/bin/samtools [04:44:25] Found java - /usr/local/bin/java [04:44:25] Found snpEff - /usr/local/bin/snpEff [04:44:25] Found samclip - /usr/local/bin/samclip [04:44:25] Found seqtk - /usr/local/bin/seqtk [04:44:25] Found parallel - /usr/local/bin/parallel [04:44:25] Found freebayes - /usr/local/bin/freebayes [04:44:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:44:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:44:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:44:25] Found vcfuniq - /usr/local/bin/vcfuniq [04:44:25] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:44:25] Found gzip - /bin/gzip [04:44:25] Found vt - /usr/local/bin/vt [04:44:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:44:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:44:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:44:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:44:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:44:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:44:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:44:26] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:44:40] This is snippy 4.6.0
Show full stderr[04:44:40] This is snippy 4.6.0 [04:44:40] Written by Torsten Seemann [04:44:40] Obtained from https://github.com/tseemann/snippy [04:44:40] Detected operating system: linux [04:44:40] Enabling bundled linux tools. [04:44:40] Found bwa - /usr/local/bin/bwa [04:44:40] Found bcftools - /usr/local/bin/bcftools [04:44:40] Found samtools - /usr/local/bin/samtools [04:44:40] Found java - /usr/local/bin/java [04:44:40] Found snpEff - /usr/local/bin/snpEff [04:44:40] Found samclip - /usr/local/bin/samclip [04:44:40] Found seqtk - /usr/local/bin/seqtk [04:44:40] Found parallel - /usr/local/bin/parallel [04:44:40] Found freebayes - /usr/local/bin/freebayes [04:44:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:44:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:44:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:44:40] Found vcfuniq - /usr/local/bin/vcfuniq [04:44:40] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:44:40] Found gzip - /bin/gzip [04:44:40] Found vt - /usr/local/bin/vt [04:44:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:44:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:44:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:44:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:44:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:44:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:44:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:44:41] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:43:37] This is snippy 4.6.0
Show full stderr[04:43:37] This is snippy 4.6.0 [04:43:37] Written by Torsten Seemann [04:43:37] Obtained from https://github.com/tseemann/snippy [04:43:37] Detected operating system: linux [04:43:37] Enabling bundled linux tools. [04:43:37] Found bwa - /usr/local/bin/bwa [04:43:37] Found bcftools - /usr/local/bin/bcftools [04:43:37] Found samtools - /usr/local/bin/samtools [04:43:37] Found java - /usr/local/bin/java [04:43:37] Found snpEff - /usr/local/bin/snpEff [04:43:37] Found samclip - /usr/local/bin/samclip [04:43:37] Found seqtk - /usr/local/bin/seqtk [04:43:37] Found parallel - /usr/local/bin/parallel [04:43:37] Found freebayes - /usr/local/bin/freebayes [04:43:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:43:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:43:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:43:37] Found vcfuniq - /usr/local/bin/vcfuniq [04:43:37] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:43:37] Found gzip - /bin/gzip [04:43:37] Found vt - /usr/local/bin/vt [04:43:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:43:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:43:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:43:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:43:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:43:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:43:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:43:38] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:42:30] This is snippy 4.6.0
Show full stderr[04:42:30] This is snippy 4.6.0 [04:42:30] Written by Torsten Seemann [04:42:30] Obtained from https://github.com/tseemann/snippy [04:42:30] Detected operating system: linux [04:42:30] Enabling bundled linux tools. [04:42:30] Found bwa - /usr/local/bin/bwa [04:42:30] Found bcftools - /usr/local/bin/bcftools [04:42:30] Found samtools - /usr/local/bin/samtools [04:42:30] Found java - /usr/local/bin/java [04:42:30] Found snpEff - /usr/local/bin/snpEff [04:42:30] Found samclip - /usr/local/bin/samclip [04:42:30] Found seqtk - /usr/local/bin/seqtk [04:42:30] Found parallel - /usr/local/bin/parallel [04:42:30] Found freebayes - /usr/local/bin/freebayes [04:42:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:42:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:42:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:42:30] Found vcfuniq - /usr/local/bin/vcfuniq [04:42:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:42:30] Found gzip - /bin/gzip [04:42:30] Found vt - /usr/local/bin/vt [04:42:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:42:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:42:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:42:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:42:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:42:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:42:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:42:31] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:54:52] This is snippy 4.6.0
Show full stderr[04:54:52] This is snippy 4.6.0 [04:54:52] Written by Torsten Seemann [04:54:52] Obtained from https://github.com/tseemann/snippy [04:54:52] Detected operating system: linux [04:54:52] Enabling bundled linux tools. [04:54:52] Found bwa - /usr/local/bin/bwa [04:54:52] Found bcftools - /usr/local/bin/bcftools [04:54:52] Found samtools - /usr/local/bin/samtools [04:54:52] Found java - /usr/local/bin/java [04:54:52] Found snpEff - /usr/local/bin/snpEff [04:54:52] Found samclip - /usr/local/bin/samclip [04:54:52] Found seqtk - /usr/local/bin/seqtk [04:54:52] Found parallel - /usr/local/bin/parallel [04:54:52] Found freebayes - /usr/local/bin/freebayes [04:54:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:54:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:54:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:54:52] Found vcfuniq - /usr/local/bin/vcfuniq [04:54:52] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:54:52] Found gzip - /bin/gzip [04:54:52] Found vt - /usr/local/bin/vt [04:54:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:54:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:54:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:54:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:54:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:54:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:54:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:54:53] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:55:09] This is snippy 4.6.0
Show full stderr[04:55:09] This is snippy 4.6.0 [04:55:09] Written by Torsten Seemann [04:55:09] Obtained from https://github.com/tseemann/snippy [04:55:09] Detected operating system: linux [04:55:09] Enabling bundled linux tools. [04:55:09] Found bwa - /usr/local/bin/bwa [04:55:09] Found bcftools - /usr/local/bin/bcftools [04:55:09] Found samtools - /usr/local/bin/samtools [04:55:09] Found java - /usr/local/bin/java [04:55:09] Found snpEff - /usr/local/bin/snpEff [04:55:09] Found samclip - /usr/local/bin/samclip [04:55:09] Found seqtk - /usr/local/bin/seqtk [04:55:09] Found parallel - /usr/local/bin/parallel [04:55:09] Found freebayes - /usr/local/bin/freebayes [04:55:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:55:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:55:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:55:09] Found vcfuniq - /usr/local/bin/vcfuniq [04:55:09] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:55:09] Found gzip - /bin/gzip [04:55:09] Found vt - /usr/local/bin/vt [04:55:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:55:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:55:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:55:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:55:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:55:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:55:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:55:11] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:55:49] This is snippy 4.6.0
Show full stderr[04:55:49] This is snippy 4.6.0 [04:55:49] Written by Torsten Seemann [04:55:49] Obtained from https://github.com/tseemann/snippy [04:55:49] Detected operating system: linux [04:55:49] Enabling bundled linux tools. [04:55:49] Found bwa - /usr/local/bin/bwa [04:55:49] Found bcftools - /usr/local/bin/bcftools [04:55:49] Found samtools - /usr/local/bin/samtools [04:55:49] Found java - /usr/local/bin/java [04:55:49] Found snpEff - /usr/local/bin/snpEff [04:55:49] Found samclip - /usr/local/bin/samclip [04:55:49] Found seqtk - /usr/local/bin/seqtk [04:55:49] Found parallel - /usr/local/bin/parallel [04:55:49] Found freebayes - /usr/local/bin/freebayes [04:55:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:55:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:55:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:55:49] Found vcfuniq - /usr/local/bin/vcfuniq [04:55:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:55:49] Found gzip - /bin/gzip [04:55:49] Found vt - /usr/local/bin/vt [04:55:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:55:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:55:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:55:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:55:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:55:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:55:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:55:51] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:57:03] This is snippy 4.6.0
Show full stderr[04:57:03] This is snippy 4.6.0 [04:57:03] Written by Torsten Seemann [04:57:03] Obtained from https://github.com/tseemann/snippy [04:57:03] Detected operating system: linux [04:57:03] Enabling bundled linux tools. [04:57:03] Found bwa - /usr/local/bin/bwa [04:57:03] Found bcftools - /usr/local/bin/bcftools [04:57:03] Found samtools - /usr/local/bin/samtools [04:57:03] Found java - /usr/local/bin/java [04:57:03] Found snpEff - /usr/local/bin/snpEff [04:57:03] Found samclip - /usr/local/bin/samclip [04:57:03] Found seqtk - /usr/local/bin/seqtk [04:57:03] Found parallel - /usr/local/bin/parallel [04:57:03] Found freebayes - /usr/local/bin/freebayes [04:57:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:57:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:57:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:57:03] Found vcfuniq - /usr/local/bin/vcfuniq [04:57:03] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:57:03] Found gzip - /bin/gzip [04:57:03] Found vt - /usr/local/bin/vt [04:57:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:57:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:57:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:57:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:57:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:57:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:57:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:57:05] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:57:09] This is snippy 4.6.0
Show full stderr[04:57:09] This is snippy 4.6.0 [04:57:09] Written by Torsten Seemann [04:57:09] Obtained from https://github.com/tseemann/snippy [04:57:09] Detected operating system: linux [04:57:09] Enabling bundled linux tools. [04:57:09] Found bwa - /usr/local/bin/bwa [04:57:09] Found bcftools - /usr/local/bin/bcftools [04:57:09] Found samtools - /usr/local/bin/samtools [04:57:09] Found java - /usr/local/bin/java [04:57:09] Found snpEff - /usr/local/bin/snpEff [04:57:09] Found samclip - /usr/local/bin/samclip [04:57:09] Found seqtk - /usr/local/bin/seqtk [04:57:09] Found parallel - /usr/local/bin/parallel [04:57:09] Found freebayes - /usr/local/bin/freebayes [04:57:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:57:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:57:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:57:09] Found vcfuniq - /usr/local/bin/vcfuniq [04:57:09] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:57:09] Found gzip - /bin/gzip [04:57:09] Found vt - /usr/local/bin/vt [04:57:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:57:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:57:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:57:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:57:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:57:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:57:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:57:10] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:57:30] This is snippy 4.6.0
Show full stderr[04:57:30] This is snippy 4.6.0 [04:57:30] Written by Torsten Seemann [04:57:30] Obtained from https://github.com/tseemann/snippy [04:57:30] Detected operating system: linux [04:57:30] Enabling bundled linux tools. [04:57:30] Found bwa - /usr/local/bin/bwa [04:57:30] Found bcftools - /usr/local/bin/bcftools [04:57:30] Found samtools - /usr/local/bin/samtools [04:57:30] Found java - /usr/local/bin/java [04:57:30] Found snpEff - /usr/local/bin/snpEff [04:57:30] Found samclip - /usr/local/bin/samclip [04:57:30] Found seqtk - /usr/local/bin/seqtk [04:57:30] Found parallel - /usr/local/bin/parallel [04:57:30] Found freebayes - /usr/local/bin/freebayes [04:57:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:57:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:57:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:57:30] Found vcfuniq - /usr/local/bin/vcfuniq [04:57:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:57:30] Found gzip - /bin/gzip [04:57:30] Found vt - /usr/local/bin/vt [04:57:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:57:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:57:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:57:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:57:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:57:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:57:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:57:31] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:57:48] This is snippy 4.6.0
Show full stderr[04:57:48] This is snippy 4.6.0 [04:57:48] Written by Torsten Seemann [04:57:48] Obtained from https://github.com/tseemann/snippy [04:57:48] Detected operating system: linux [04:57:48] Enabling bundled linux tools. [04:57:48] Found bwa - /usr/local/bin/bwa [04:57:48] Found bcftools - /usr/local/bin/bcftools [04:57:48] Found samtools - /usr/local/bin/samtools [04:57:48] Found java - /usr/local/bin/java [04:57:48] Found snpEff - /usr/local/bin/snpEff [04:57:48] Found samclip - /usr/local/bin/samclip [04:57:48] Found seqtk - /usr/local/bin/seqtk [04:57:48] Found parallel - /usr/local/bin/parallel [04:57:48] Found freebayes - /usr/local/bin/freebayes [04:57:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:57:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:57:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:57:48] Found vcfuniq - /usr/local/bin/vcfuniq [04:57:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:57:49] Found gzip - /bin/gzip [04:57:49] Found vt - /usr/local/bin/vt [04:57:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:57:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:57:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:57:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:57:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:57:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:57:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:57:50] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:58:03] This is snippy 4.6.0
Show full stderr[04:58:03] This is snippy 4.6.0 [04:58:03] Written by Torsten Seemann [04:58:03] Obtained from https://github.com/tseemann/snippy [04:58:03] Detected operating system: linux [04:58:03] Enabling bundled linux tools. [04:58:03] Found bwa - /usr/local/bin/bwa [04:58:03] Found bcftools - /usr/local/bin/bcftools [04:58:03] Found samtools - /usr/local/bin/samtools [04:58:03] Found java - /usr/local/bin/java [04:58:03] Found snpEff - /usr/local/bin/snpEff [04:58:03] Found samclip - /usr/local/bin/samclip [04:58:03] Found seqtk - /usr/local/bin/seqtk [04:58:03] Found parallel - /usr/local/bin/parallel [04:58:03] Found freebayes - /usr/local/bin/freebayes [04:58:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:58:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:58:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:58:03] Found vcfuniq - /usr/local/bin/vcfuniq [04:58:03] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:58:03] Found gzip - /bin/gzip [04:58:03] Found vt - /usr/local/bin/vt [04:58:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:58:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:58:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:58:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:58:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:58:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:58:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:58:04] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:56:45] This is snippy 4.6.0
Show full stderr[04:56:45] This is snippy 4.6.0 [04:56:45] Written by Torsten Seemann [04:56:45] Obtained from https://github.com/tseemann/snippy [04:56:45] Detected operating system: linux [04:56:45] Enabling bundled linux tools. [04:56:45] Found bwa - /usr/local/bin/bwa [04:56:45] Found bcftools - /usr/local/bin/bcftools [04:56:45] Found samtools - /usr/local/bin/samtools [04:56:45] Found java - /usr/local/bin/java [04:56:45] Found snpEff - /usr/local/bin/snpEff [04:56:45] Found samclip - /usr/local/bin/samclip [04:56:45] Found seqtk - /usr/local/bin/seqtk [04:56:45] Found parallel - /usr/local/bin/parallel [04:56:45] Found freebayes - /usr/local/bin/freebayes [04:56:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:56:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:56:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:56:45] Found vcfuniq - /usr/local/bin/vcfuniq [04:56:45] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:56:45] Found gzip - /bin/gzip [04:56:45] Found vt - /usr/local/bin/vt [04:56:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:56:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:56:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:56:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:56:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:56:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:56:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:56:47] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:58:21] This is snippy 4.6.0
Show full stderr[04:58:21] This is snippy 4.6.0 [04:58:21] Written by Torsten Seemann [04:58:21] Obtained from https://github.com/tseemann/snippy [04:58:21] Detected operating system: linux [04:58:21] Enabling bundled linux tools. [04:58:21] Found bwa - /usr/local/bin/bwa [04:58:21] Found bcftools - /usr/local/bin/bcftools [04:58:21] Found samtools - /usr/local/bin/samtools [04:58:21] Found java - /usr/local/bin/java [04:58:21] Found snpEff - /usr/local/bin/snpEff [04:58:21] Found samclip - /usr/local/bin/samclip [04:58:21] Found seqtk - /usr/local/bin/seqtk [04:58:21] Found parallel - /usr/local/bin/parallel [04:58:21] Found freebayes - /usr/local/bin/freebayes [04:58:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:58:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:58:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:58:21] Found vcfuniq - /usr/local/bin/vcfuniq [04:58:21] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:58:21] Found gzip - /bin/gzip [04:58:21] Found vt - /usr/local/bin/vt [04:58:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:58:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:58:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:58:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:58:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:58:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:58:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:58:22] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:58:33] This is snippy 4.6.0
Show full stderr[04:58:33] This is snippy 4.6.0 [04:58:33] Written by Torsten Seemann [04:58:33] Obtained from https://github.com/tseemann/snippy [04:58:33] Detected operating system: linux [04:58:33] Enabling bundled linux tools. [04:58:33] Found bwa - /usr/local/bin/bwa [04:58:33] Found bcftools - /usr/local/bin/bcftools [04:58:33] Found samtools - /usr/local/bin/samtools [04:58:33] Found java - /usr/local/bin/java [04:58:33] Found snpEff - /usr/local/bin/snpEff [04:58:33] Found samclip - /usr/local/bin/samclip [04:58:33] Found seqtk - /usr/local/bin/seqtk [04:58:33] Found parallel - /usr/local/bin/parallel [04:58:33] Found freebayes - /usr/local/bin/freebayes [04:58:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:58:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:58:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:58:33] Found vcfuniq - /usr/local/bin/vcfuniq [04:58:33] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:58:33] Found gzip - /bin/gzip [04:58:33] Found vt - /usr/local/bin/vt [04:58:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:58:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:58:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:58:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:58:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:58:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:58:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:58:34] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:59:06] This is snippy 4.6.0
Show full stderr[04:59:06] This is snippy 4.6.0 [04:59:06] Written by Torsten Seemann [04:59:06] Obtained from https://github.com/tseemann/snippy [04:59:06] Detected operating system: linux [04:59:06] Enabling bundled linux tools. [04:59:06] Found bwa - /usr/local/bin/bwa [04:59:06] Found bcftools - /usr/local/bin/bcftools [04:59:06] Found samtools - /usr/local/bin/samtools [04:59:06] Found java - /usr/local/bin/java [04:59:06] Found snpEff - /usr/local/bin/snpEff [04:59:06] Found samclip - /usr/local/bin/samclip [04:59:06] Found seqtk - /usr/local/bin/seqtk [04:59:06] Found parallel - /usr/local/bin/parallel [04:59:06] Found freebayes - /usr/local/bin/freebayes [04:59:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:59:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:59:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:59:06] Found vcfuniq - /usr/local/bin/vcfuniq [04:59:06] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:59:06] Found gzip - /bin/gzip [04:59:06] Found vt - /usr/local/bin/vt [04:59:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:59:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:59:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:59:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:59:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:59:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:59:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:59:07] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:56:54] This is snippy 4.6.0
Show full stderr[04:56:54] This is snippy 4.6.0 [04:56:54] Written by Torsten Seemann [04:56:54] Obtained from https://github.com/tseemann/snippy [04:56:54] Detected operating system: linux [04:56:54] Enabling bundled linux tools. [04:56:54] Found bwa - /usr/local/bin/bwa [04:56:54] Found bcftools - /usr/local/bin/bcftools [04:56:54] Found samtools - /usr/local/bin/samtools [04:56:54] Found java - /usr/local/bin/java [04:56:54] Found snpEff - /usr/local/bin/snpEff [04:56:54] Found samclip - /usr/local/bin/samclip [04:56:54] Found seqtk - /usr/local/bin/seqtk [04:56:54] Found parallel - /usr/local/bin/parallel [04:56:54] Found freebayes - /usr/local/bin/freebayes [04:56:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:56:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:56:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:56:54] Found vcfuniq - /usr/local/bin/vcfuniq [04:56:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:56:54] Found gzip - /bin/gzip [04:56:54] Found vt - /usr/local/bin/vt [04:56:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:56:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:56:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:56:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:56:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:56:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:56:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:56:55] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:57:21] This is snippy 4.6.0
Show full stderr[04:57:21] This is snippy 4.6.0 [04:57:21] Written by Torsten Seemann [04:57:21] Obtained from https://github.com/tseemann/snippy [04:57:21] Detected operating system: linux [04:57:21] Enabling bundled linux tools. [04:57:21] Found bwa - /usr/local/bin/bwa [04:57:21] Found bcftools - /usr/local/bin/bcftools [04:57:21] Found samtools - /usr/local/bin/samtools [04:57:21] Found java - /usr/local/bin/java [04:57:21] Found snpEff - /usr/local/bin/snpEff [04:57:21] Found samclip - /usr/local/bin/samclip [04:57:21] Found seqtk - /usr/local/bin/seqtk [04:57:21] Found parallel - /usr/local/bin/parallel [04:57:21] Found freebayes - /usr/local/bin/freebayes [04:57:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:57:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:57:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:57:21] Found vcfuniq - /usr/local/bin/vcfuniq [04:57:21] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:57:21] Found gzip - /bin/gzip [04:57:21] Found vt - /usr/local/bin/vt [04:57:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:57:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:57:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:57:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:57:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:57:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:57:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:57:22] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:57:24] This is snippy 4.6.0
Show full stderr[04:57:24] This is snippy 4.6.0 [04:57:24] Written by Torsten Seemann [04:57:24] Obtained from https://github.com/tseemann/snippy [04:57:24] Detected operating system: linux [04:57:24] Enabling bundled linux tools. [04:57:24] Found bwa - /usr/local/bin/bwa [04:57:24] Found bcftools - /usr/local/bin/bcftools [04:57:24] Found samtools - /usr/local/bin/samtools [04:57:24] Found java - /usr/local/bin/java [04:57:24] Found snpEff - /usr/local/bin/snpEff [04:57:24] Found samclip - /usr/local/bin/samclip [04:57:24] Found seqtk - /usr/local/bin/seqtk [04:57:24] Found parallel - /usr/local/bin/parallel [04:57:24] Found freebayes - /usr/local/bin/freebayes [04:57:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:57:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:57:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:57:24] Found vcfuniq - /usr/local/bin/vcfuniq [04:57:24] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:57:24] Found gzip - /bin/gzip [04:57:24] Found vt - /usr/local/bin/vt [04:57:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:57:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:57:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:57:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:57:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:57:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:57:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:57:25] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:58:48] This is snippy 4.6.0
Show full stderr[04:58:48] This is snippy 4.6.0 [04:58:48] Written by Torsten Seemann [04:58:48] Obtained from https://github.com/tseemann/snippy [04:58:48] Detected operating system: linux [04:58:48] Enabling bundled linux tools. [04:58:48] Found bwa - /usr/local/bin/bwa [04:58:48] Found bcftools - /usr/local/bin/bcftools [04:58:48] Found samtools - /usr/local/bin/samtools [04:58:48] Found java - /usr/local/bin/java [04:58:48] Found snpEff - /usr/local/bin/snpEff [04:58:48] Found samclip - /usr/local/bin/samclip [04:58:48] Found seqtk - /usr/local/bin/seqtk [04:58:48] Found parallel - /usr/local/bin/parallel [04:58:48] Found freebayes - /usr/local/bin/freebayes [04:58:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:58:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:58:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:58:48] Found vcfuniq - /usr/local/bin/vcfuniq [04:58:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:58:48] Found gzip - /bin/gzip [04:58:48] Found vt - /usr/local/bin/vt [04:58:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:58:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:58:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:58:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:58:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:58:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:58:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:58:49] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:59:18] This is snippy 4.6.0
Show full stderr[04:59:18] This is snippy 4.6.0 [04:59:18] Written by Torsten Seemann [04:59:18] Obtained from https://github.com/tseemann/snippy [04:59:18] Detected operating system: linux [04:59:18] Enabling bundled linux tools. [04:59:18] Found bwa - /usr/local/bin/bwa [04:59:18] Found bcftools - /usr/local/bin/bcftools [04:59:18] Found samtools - /usr/local/bin/samtools [04:59:18] Found java - /usr/local/bin/java [04:59:18] Found snpEff - /usr/local/bin/snpEff [04:59:18] Found samclip - /usr/local/bin/samclip [04:59:18] Found seqtk - /usr/local/bin/seqtk [04:59:18] Found parallel - /usr/local/bin/parallel [04:59:18] Found freebayes - /usr/local/bin/freebayes [04:59:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:59:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:59:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:59:18] Found vcfuniq - /usr/local/bin/vcfuniq [04:59:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:59:18] Found gzip - /bin/gzip [04:59:18] Found vt - /usr/local/bin/vt [04:59:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:59:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:59:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:59:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:59:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:59:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:59:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:59:19] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:59:37] This is snippy 4.6.0
Show full stderr[04:59:37] This is snippy 4.6.0 [04:59:37] Written by Torsten Seemann [04:59:37] Obtained from https://github.com/tseemann/snippy [04:59:37] Detected operating system: linux [04:59:37] Enabling bundled linux tools. [04:59:37] Found bwa - /usr/local/bin/bwa [04:59:37] Found bcftools - /usr/local/bin/bcftools [04:59:37] Found samtools - /usr/local/bin/samtools [04:59:37] Found java - /usr/local/bin/java [04:59:37] Found snpEff - /usr/local/bin/snpEff [04:59:37] Found samclip - /usr/local/bin/samclip [04:59:37] Found seqtk - /usr/local/bin/seqtk [04:59:37] Found parallel - /usr/local/bin/parallel [04:59:37] Found freebayes - /usr/local/bin/freebayes [04:59:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:59:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:59:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:59:37] Found vcfuniq - /usr/local/bin/vcfuniq [04:59:37] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:59:37] Found gzip - /bin/gzip [04:59:37] Found vt - /usr/local/bin/vt [04:59:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:59:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:59:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:59:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:59:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:59:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:59:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:59:38] Please supply a reference FASTA/GBK/EMBL file with --reference
2[05:00:01] This is snippy 4.6.0
Show full stderr[05:00:01] This is snippy 4.6.0 [05:00:01] Written by Torsten Seemann [05:00:01] Obtained from https://github.com/tseemann/snippy [05:00:01] Detected operating system: linux [05:00:01] Enabling bundled linux tools. [05:00:01] Found bwa - /usr/local/bin/bwa [05:00:01] Found bcftools - /usr/local/bin/bcftools [05:00:01] Found samtools - /usr/local/bin/samtools [05:00:01] Found java - /usr/local/bin/java [05:00:01] Found snpEff - /usr/local/bin/snpEff [05:00:01] Found samclip - /usr/local/bin/samclip [05:00:01] Found seqtk - /usr/local/bin/seqtk [05:00:01] Found parallel - /usr/local/bin/parallel [05:00:01] Found freebayes - /usr/local/bin/freebayes [05:00:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:00:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:00:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:00:01] Found vcfuniq - /usr/local/bin/vcfuniq [05:00:01] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:00:01] Found gzip - /bin/gzip [05:00:01] Found vt - /usr/local/bin/vt [05:00:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:00:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:00:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:00:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:00:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:00:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:00:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:00:02] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:56:57] This is snippy 4.6.0
Show full stderr[04:56:57] This is snippy 4.6.0 [04:56:57] Written by Torsten Seemann [04:56:57] Obtained from https://github.com/tseemann/snippy [04:56:57] Detected operating system: linux [04:56:57] Enabling bundled linux tools. [04:56:57] Found bwa - /usr/local/bin/bwa [04:56:57] Found bcftools - /usr/local/bin/bcftools [04:56:57] Found samtools - /usr/local/bin/samtools [04:56:57] Found java - /usr/local/bin/java [04:56:57] Found snpEff - /usr/local/bin/snpEff [04:56:57] Found samclip - /usr/local/bin/samclip [04:56:57] Found seqtk - /usr/local/bin/seqtk [04:56:57] Found parallel - /usr/local/bin/parallel [04:56:57] Found freebayes - /usr/local/bin/freebayes [04:56:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:56:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:56:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:56:57] Found vcfuniq - /usr/local/bin/vcfuniq [04:56:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:56:57] Found gzip - /bin/gzip [04:56:57] Found vt - /usr/local/bin/vt [04:56:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:56:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:56:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:56:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:56:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:56:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:56:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:56:58] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:59:48] This is snippy 4.6.0
Show full stderr[04:59:48] This is snippy 4.6.0 [04:59:48] Written by Torsten Seemann [04:59:48] Obtained from https://github.com/tseemann/snippy [04:59:48] Detected operating system: linux [04:59:48] Enabling bundled linux tools. [04:59:48] Found bwa - /usr/local/bin/bwa [04:59:48] Found bcftools - /usr/local/bin/bcftools [04:59:48] Found samtools - /usr/local/bin/samtools [04:59:48] Found java - /usr/local/bin/java [04:59:48] Found snpEff - /usr/local/bin/snpEff [04:59:48] Found samclip - /usr/local/bin/samclip [04:59:48] Found seqtk - /usr/local/bin/seqtk [04:59:48] Found parallel - /usr/local/bin/parallel [04:59:48] Found freebayes - /usr/local/bin/freebayes [04:59:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:59:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:59:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:59:48] Found vcfuniq - /usr/local/bin/vcfuniq [04:59:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:59:48] Found gzip - /bin/gzip [04:59:48] Found vt - /usr/local/bin/vt [04:59:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:59:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:59:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:59:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:59:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:59:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:59:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:59:49] Please supply a reference FASTA/GBK/EMBL file with --reference
2[05:00:15] This is snippy 4.6.0
Show full stderr[05:00:15] This is snippy 4.6.0 [05:00:15] Written by Torsten Seemann [05:00:15] Obtained from https://github.com/tseemann/snippy [05:00:15] Detected operating system: linux [05:00:15] Enabling bundled linux tools. [05:00:15] Found bwa - /usr/local/bin/bwa [05:00:15] Found bcftools - /usr/local/bin/bcftools [05:00:15] Found samtools - /usr/local/bin/samtools [05:00:15] Found java - /usr/local/bin/java [05:00:15] Found snpEff - /usr/local/bin/snpEff [05:00:15] Found samclip - /usr/local/bin/samclip [05:00:15] Found seqtk - /usr/local/bin/seqtk [05:00:15] Found parallel - /usr/local/bin/parallel [05:00:15] Found freebayes - /usr/local/bin/freebayes [05:00:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:00:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:00:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:00:15] Found vcfuniq - /usr/local/bin/vcfuniq [05:00:15] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:00:15] Found gzip - /bin/gzip [05:00:15] Found vt - /usr/local/bin/vt [05:00:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:00:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:00:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:00:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:00:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:00:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:00:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:00:16] Please supply a reference FASTA/GBK/EMBL file with --reference
2[05:01:15] This is snippy 4.6.0
Show full stderr[05:01:15] This is snippy 4.6.0 [05:01:15] Written by Torsten Seemann [05:01:15] Obtained from https://github.com/tseemann/snippy [05:01:15] Detected operating system: linux [05:01:15] Enabling bundled linux tools. [05:01:15] Found bwa - /usr/local/bin/bwa [05:01:15] Found bcftools - /usr/local/bin/bcftools [05:01:15] Found samtools - /usr/local/bin/samtools [05:01:15] Found java - /usr/local/bin/java [05:01:15] Found snpEff - /usr/local/bin/snpEff [05:01:15] Found samclip - /usr/local/bin/samclip [05:01:15] Found seqtk - /usr/local/bin/seqtk [05:01:15] Found parallel - /usr/local/bin/parallel [05:01:15] Found freebayes - /usr/local/bin/freebayes [05:01:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:01:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:01:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:01:15] Found vcfuniq - /usr/local/bin/vcfuniq [05:01:15] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:01:15] Found gzip - /bin/gzip [05:01:15] Found vt - /usr/local/bin/vt [05:01:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:01:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:01:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:01:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:01:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:01:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:01:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:01:16] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:58:39] This is snippy 4.6.0
Show full stderr[04:58:39] This is snippy 4.6.0 [04:58:39] Written by Torsten Seemann [04:58:39] Obtained from https://github.com/tseemann/snippy [04:58:39] Detected operating system: linux [04:58:39] Enabling bundled linux tools. [04:58:39] Found bwa - /usr/local/bin/bwa [04:58:39] Found bcftools - /usr/local/bin/bcftools [04:58:39] Found samtools - /usr/local/bin/samtools [04:58:39] Found java - /usr/local/bin/java [04:58:39] Found snpEff - /usr/local/bin/snpEff [04:58:39] Found samclip - /usr/local/bin/samclip [04:58:39] Found seqtk - /usr/local/bin/seqtk [04:58:39] Found parallel - /usr/local/bin/parallel [04:58:39] Found freebayes - /usr/local/bin/freebayes [04:58:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:58:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:58:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:58:40] Found vcfuniq - /usr/local/bin/vcfuniq [04:58:40] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:58:40] Found gzip - /bin/gzip [04:58:40] Found vt - /usr/local/bin/vt [04:58:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:58:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:58:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:58:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:58:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:58:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:58:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:58:40] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:59:03] This is snippy 4.6.0
Show full stderr[04:59:03] This is snippy 4.6.0 [04:59:03] Written by Torsten Seemann [04:59:03] Obtained from https://github.com/tseemann/snippy [04:59:03] Detected operating system: linux [04:59:03] Enabling bundled linux tools. [04:59:03] Found bwa - /usr/local/bin/bwa [04:59:03] Found bcftools - /usr/local/bin/bcftools [04:59:03] Found samtools - /usr/local/bin/samtools [04:59:03] Found java - /usr/local/bin/java [04:59:03] Found snpEff - /usr/local/bin/snpEff [04:59:03] Found samclip - /usr/local/bin/samclip [04:59:03] Found seqtk - /usr/local/bin/seqtk [04:59:03] Found parallel - /usr/local/bin/parallel [04:59:03] Found freebayes - /usr/local/bin/freebayes [04:59:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:59:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:59:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:59:03] Found vcfuniq - /usr/local/bin/vcfuniq [04:59:03] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:59:03] Found gzip - /bin/gzip [04:59:03] Found vt - /usr/local/bin/vt [04:59:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:59:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:59:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:59:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:59:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:59:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:59:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:59:04] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:59:33] This is snippy 4.6.0
Show full stderr[04:59:33] This is snippy 4.6.0 [04:59:33] Written by Torsten Seemann [04:59:33] Obtained from https://github.com/tseemann/snippy [04:59:33] Detected operating system: linux [04:59:33] Enabling bundled linux tools. [04:59:33] Found bwa - /usr/local/bin/bwa [04:59:33] Found bcftools - /usr/local/bin/bcftools [04:59:33] Found samtools - /usr/local/bin/samtools [04:59:33] Found java - /usr/local/bin/java [04:59:33] Found snpEff - /usr/local/bin/snpEff [04:59:33] Found samclip - /usr/local/bin/samclip [04:59:33] Found seqtk - /usr/local/bin/seqtk [04:59:33] Found parallel - /usr/local/bin/parallel [04:59:33] Found freebayes - /usr/local/bin/freebayes [04:59:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:59:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:59:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:59:33] Found vcfuniq - /usr/local/bin/vcfuniq [04:59:33] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:59:33] Found gzip - /bin/gzip [04:59:33] Found vt - /usr/local/bin/vt [04:59:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:59:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:59:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:59:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:59:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:59:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:59:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:59:34] Please supply a reference FASTA/GBK/EMBL file with --reference
2[04:59:54] This is snippy 4.6.0
Show full stderr[04:59:54] This is snippy 4.6.0 [04:59:54] Written by Torsten Seemann [04:59:54] Obtained from https://github.com/tseemann/snippy [04:59:54] Detected operating system: linux [04:59:54] Enabling bundled linux tools. [04:59:54] Found bwa - /usr/local/bin/bwa [04:59:54] Found bcftools - /usr/local/bin/bcftools [04:59:54] Found samtools - /usr/local/bin/samtools [04:59:54] Found java - /usr/local/bin/java [04:59:54] Found snpEff - /usr/local/bin/snpEff [04:59:54] Found samclip - /usr/local/bin/samclip [04:59:54] Found seqtk - /usr/local/bin/seqtk [04:59:54] Found parallel - /usr/local/bin/parallel [04:59:54] Found freebayes - /usr/local/bin/freebayes [04:59:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:59:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:59:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:59:54] Found vcfuniq - /usr/local/bin/vcfuniq [04:59:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:59:54] Found gzip - /bin/gzip [04:59:54] Found vt - /usr/local/bin/vt [04:59:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:59:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:59:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:59:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:59:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:59:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:59:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:59:55] Please supply a reference FASTA/GBK/EMBL file with --reference
2[05:03:03] This is snippy 4.6.0
Show full stderr[05:03:03] This is snippy 4.6.0 [05:03:03] Written by Torsten Seemann [05:03:03] Obtained from https://github.com/tseemann/snippy [05:03:03] Detected operating system: linux [05:03:03] Enabling bundled linux tools. [05:03:03] Found bwa - /usr/local/bin/bwa [05:03:03] Found bcftools - /usr/local/bin/bcftools [05:03:03] Found samtools - /usr/local/bin/samtools [05:03:03] Found java - /usr/local/bin/java [05:03:03] Found snpEff - /usr/local/bin/snpEff [05:03:03] Found samclip - /usr/local/bin/samclip [05:03:03] Found seqtk - /usr/local/bin/seqtk [05:03:03] Found parallel - /usr/local/bin/parallel [05:03:03] Found freebayes - /usr/local/bin/freebayes [05:03:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:03:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:03:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:03:03] Found vcfuniq - /usr/local/bin/vcfuniq [05:03:03] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:03:03] Found gzip - /bin/gzip [05:03:03] Found vt - /usr/local/bin/vt [05:03:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:03:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:03:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:03:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:03:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:03:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:03:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:03:03] Please supply a reference FASTA/GBK/EMBL file with --reference
2[05:04:06] This is snippy 4.6.0
Show full stderr[05:04:06] This is snippy 4.6.0 [05:04:06] Written by Torsten Seemann [05:04:06] Obtained from https://github.com/tseemann/snippy [05:04:06] Detected operating system: linux [05:04:06] Enabling bundled linux tools. [05:04:06] Found bwa - /usr/local/bin/bwa [05:04:06] Found bcftools - /usr/local/bin/bcftools [05:04:06] Found samtools - /usr/local/bin/samtools [05:04:06] Found java - /usr/local/bin/java [05:04:06] Found snpEff - /usr/local/bin/snpEff [05:04:06] Found samclip - /usr/local/bin/samclip [05:04:06] Found seqtk - /usr/local/bin/seqtk [05:04:06] Found parallel - /usr/local/bin/parallel [05:04:06] Found freebayes - /usr/local/bin/freebayes [05:04:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:04:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:04:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:04:06] Found vcfuniq - /usr/local/bin/vcfuniq [05:04:06] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:04:06] Found gzip - /bin/gzip [05:04:06] Found vt - /usr/local/bin/vt [05:04:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:04:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:04:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:04:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:04:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:04:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:04:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:04:07] Please supply a reference FASTA/GBK/EMBL file with --reference
2[05:04:23] This is snippy 4.6.0
Show full stderr[05:04:23] This is snippy 4.6.0 [05:04:23] Written by Torsten Seemann [05:04:23] Obtained from https://github.com/tseemann/snippy [05:04:23] Detected operating system: linux [05:04:23] Enabling bundled linux tools. [05:04:23] Found bwa - /usr/local/bin/bwa [05:04:23] Found bcftools - /usr/local/bin/bcftools [05:04:23] Found samtools - /usr/local/bin/samtools [05:04:23] Found java - /usr/local/bin/java [05:04:23] Found snpEff - /usr/local/bin/snpEff [05:04:23] Found samclip - /usr/local/bin/samclip [05:04:23] Found seqtk - /usr/local/bin/seqtk [05:04:23] Found parallel - /usr/local/bin/parallel [05:04:23] Found freebayes - /usr/local/bin/freebayes [05:04:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:04:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:04:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:04:23] Found vcfuniq - /usr/local/bin/vcfuniq [05:04:23] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:04:23] Found gzip - /bin/gzip [05:04:23] Found vt - /usr/local/bin/vt [05:04:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:04:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:04:23] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:04:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:04:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:04:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:04:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:04:25] Please supply a reference FASTA/GBK/EMBL file with --reference
2[05:04:32] This is snippy 4.6.0
Show full stderr[05:04:32] This is snippy 4.6.0 [05:04:32] Written by Torsten Seemann [05:04:32] Obtained from https://github.com/tseemann/snippy [05:04:32] Detected operating system: linux [05:04:32] Enabling bundled linux tools. [05:04:32] Found bwa - /usr/local/bin/bwa [05:04:32] Found bcftools - /usr/local/bin/bcftools [05:04:32] Found samtools - /usr/local/bin/samtools [05:04:32] Found java - /usr/local/bin/java [05:04:32] Found snpEff - /usr/local/bin/snpEff [05:04:32] Found samclip - /usr/local/bin/samclip [05:04:32] Found seqtk - /usr/local/bin/seqtk [05:04:32] Found parallel - /usr/local/bin/parallel [05:04:32] Found freebayes - /usr/local/bin/freebayes [05:04:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:04:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:04:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:04:32] Found vcfuniq - /usr/local/bin/vcfuniq [05:04:32] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:04:32] Found gzip - /bin/gzip [05:04:32] Found vt - /usr/local/bin/vt [05:04:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:04:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:04:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:04:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:04:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:04:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:04:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:04:33] Please supply a reference FASTA/GBK/EMBL file with --reference
2[05:01:52] This is snippy 4.6.0
Show full stderr[05:01:52] This is snippy 4.6.0 [05:01:52] Written by Torsten Seemann [05:01:52] Obtained from https://github.com/tseemann/snippy [05:01:52] Detected operating system: linux [05:01:52] Enabling bundled linux tools. [05:01:52] Found bwa - /usr/local/bin/bwa [05:01:52] Found bcftools - /usr/local/bin/bcftools [05:01:52] Found samtools - /usr/local/bin/samtools [05:01:52] Found java - /usr/local/bin/java [05:01:52] Found snpEff - /usr/local/bin/snpEff [05:01:52] Found samclip - /usr/local/bin/samclip [05:01:52] Found seqtk - /usr/local/bin/seqtk [05:01:52] Found parallel - /usr/local/bin/parallel [05:01:52] Found freebayes - /usr/local/bin/freebayes [05:01:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:01:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:01:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:01:52] Found vcfuniq - /usr/local/bin/vcfuniq [05:01:52] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:01:52] Found gzip - /bin/gzip [05:01:52] Found vt - /usr/local/bin/vt [05:01:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:01:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:01:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:01:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:01:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:01:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:01:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:01:53] Please supply a reference FASTA/GBK/EMBL file with --reference
2[05:03:16] This is snippy 4.6.0
Show full stderr[05:03:16] This is snippy 4.6.0 [05:03:16] Written by Torsten Seemann [05:03:16] Obtained from https://github.com/tseemann/snippy [05:03:16] Detected operating system: linux [05:03:16] Enabling bundled linux tools. [05:03:16] Found bwa - /usr/local/bin/bwa [05:03:16] Found bcftools - /usr/local/bin/bcftools [05:03:17] Found samtools - /usr/local/bin/samtools [05:03:17] Found java - /usr/local/bin/java [05:03:17] Found snpEff - /usr/local/bin/snpEff [05:03:17] Found samclip - /usr/local/bin/samclip [05:03:17] Found seqtk - /usr/local/bin/seqtk [05:03:17] Found parallel - /usr/local/bin/parallel [05:03:17] Found freebayes - /usr/local/bin/freebayes [05:03:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:03:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:03:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:03:17] Found vcfuniq - /usr/local/bin/vcfuniq [05:03:17] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:03:17] Found gzip - /bin/gzip [05:03:17] Found vt - /usr/local/bin/vt [05:03:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:03:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:03:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:03:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:03:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:03:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:03:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:03:17] Please supply a reference FASTA/GBK/EMBL file with --reference
2[05:04:17] This is snippy 4.6.0
Show full stderr[05:04:17] This is snippy 4.6.0 [05:04:17] Written by Torsten Seemann [05:04:17] Obtained from https://github.com/tseemann/snippy [05:04:17] Detected operating system: linux [05:04:17] Enabling bundled linux tools. [05:04:17] Found bwa - /usr/local/bin/bwa [05:04:17] Found bcftools - /usr/local/bin/bcftools [05:04:17] Found samtools - /usr/local/bin/samtools [05:04:17] Found java - /usr/local/bin/java [05:04:17] Found snpEff - /usr/local/bin/snpEff [05:04:17] Found samclip - /usr/local/bin/samclip [05:04:17] Found seqtk - /usr/local/bin/seqtk [05:04:17] Found parallel - /usr/local/bin/parallel [05:04:17] Found freebayes - /usr/local/bin/freebayes [05:04:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:04:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:04:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:04:17] Found vcfuniq - /usr/local/bin/vcfuniq [05:04:17] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:04:17] Found gzip - /bin/gzip [05:04:17] Found vt - /usr/local/bin/vt [05:04:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:04:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:04:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:04:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:04:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:04:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:04:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:04:18] Please supply a reference FASTA/GBK/EMBL file with --reference
2[05:06:46] This is snippy 4.6.0
Show full stderr[05:06:46] This is snippy 4.6.0 [05:06:46] Written by Torsten Seemann [05:06:46] Obtained from https://github.com/tseemann/snippy [05:06:46] Detected operating system: linux [05:06:46] Enabling bundled linux tools. [05:06:46] Found bwa - /usr/local/bin/bwa [05:06:46] Found bcftools - /usr/local/bin/bcftools [05:06:46] Found samtools - /usr/local/bin/samtools [05:06:46] Found java - /usr/local/bin/java [05:06:46] Found snpEff - /usr/local/bin/snpEff [05:06:46] Found samclip - /usr/local/bin/samclip [05:06:46] Found seqtk - /usr/local/bin/seqtk [05:06:46] Found parallel - /usr/local/bin/parallel [05:06:46] Found freebayes - /usr/local/bin/freebayes [05:06:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:06:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:06:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:06:46] Found vcfuniq - /usr/local/bin/vcfuniq [05:06:46] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:06:46] Found gzip - /bin/gzip [05:06:46] Found vt - /usr/local/bin/vt [05:06:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:06:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:06:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:06:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:06:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:06:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:06:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:06:47] Please supply a reference FASTA/GBK/EMBL file with --reference
2[05:04:20] This is snippy 4.6.0
Show full stderr[05:04:20] This is snippy 4.6.0 [05:04:20] Written by Torsten Seemann [05:04:20] Obtained from https://github.com/tseemann/snippy [05:04:20] Detected operating system: linux [05:04:20] Enabling bundled linux tools. [05:04:20] Found bwa - /usr/local/bin/bwa [05:04:20] Found bcftools - /usr/local/bin/bcftools [05:04:20] Found samtools - /usr/local/bin/samtools [05:04:20] Found java - /usr/local/bin/java [05:04:20] Found snpEff - /usr/local/bin/snpEff [05:04:20] Found samclip - /usr/local/bin/samclip [05:04:20] Found seqtk - /usr/local/bin/seqtk [05:04:20] Found parallel - /usr/local/bin/parallel [05:04:20] Found freebayes - /usr/local/bin/freebayes [05:04:20] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:04:20] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:04:20] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:04:20] Found vcfuniq - /usr/local/bin/vcfuniq [05:04:20] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:04:20] Found gzip - /bin/gzip [05:04:20] Found vt - /usr/local/bin/vt [05:04:20] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:04:20] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:04:20] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:04:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:04:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:04:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:04:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:04:21] Please supply a reference FASTA/GBK/EMBL file with --reference
2[05:04:35] This is snippy 4.6.0
Show full stderr[05:04:35] This is snippy 4.6.0 [05:04:35] Written by Torsten Seemann [05:04:35] Obtained from https://github.com/tseemann/snippy [05:04:35] Detected operating system: linux [05:04:35] Enabling bundled linux tools. [05:04:35] Found bwa - /usr/local/bin/bwa [05:04:35] Found bcftools - /usr/local/bin/bcftools [05:04:35] Found samtools - /usr/local/bin/samtools [05:04:35] Found java - /usr/local/bin/java [05:04:35] Found snpEff - /usr/local/bin/snpEff [05:04:35] Found samclip - /usr/local/bin/samclip [05:04:35] Found seqtk - /usr/local/bin/seqtk [05:04:35] Found parallel - /usr/local/bin/parallel [05:04:35] Found freebayes - /usr/local/bin/freebayes [05:04:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:04:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:04:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:04:35] Found vcfuniq - /usr/local/bin/vcfuniq [05:04:35] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:04:35] Found gzip - /bin/gzip [05:04:35] Found vt - /usr/local/bin/vt [05:04:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:04:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:04:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:04:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:04:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:04:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:04:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:04:36] Please supply a reference FASTA/GBK/EMBL file with --reference
2[05:04:47] This is snippy 4.6.0
Show full stderr[05:04:47] This is snippy 4.6.0 [05:04:47] Written by Torsten Seemann [05:04:47] Obtained from https://github.com/tseemann/snippy [05:04:47] Detected operating system: linux [05:04:47] Enabling bundled linux tools. [05:04:47] Found bwa - /usr/local/bin/bwa [05:04:47] Found bcftools - /usr/local/bin/bcftools [05:04:47] Found samtools - /usr/local/bin/samtools [05:04:47] Found java - /usr/local/bin/java [05:04:47] Found snpEff - /usr/local/bin/snpEff [05:04:47] Found samclip - /usr/local/bin/samclip [05:04:47] Found seqtk - /usr/local/bin/seqtk [05:04:47] Found parallel - /usr/local/bin/parallel [05:04:47] Found freebayes - /usr/local/bin/freebayes [05:04:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:04:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:04:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:04:47] Found vcfuniq - /usr/local/bin/vcfuniq [05:04:47] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:04:47] Found gzip - /bin/gzip [05:04:47] Found vt - /usr/local/bin/vt [05:04:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:04:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:04:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:04:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:04:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:04:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:04:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:04:48] Please supply a reference FASTA/GBK/EMBL file with --reference
2[05:07:21] This is snippy 4.6.0
Show full stderr[05:07:21] This is snippy 4.6.0 [05:07:21] Written by Torsten Seemann [05:07:21] Obtained from https://github.com/tseemann/snippy [05:07:21] Detected operating system: linux [05:07:21] Enabling bundled linux tools. [05:07:21] Found bwa - /usr/local/bin/bwa [05:07:21] Found bcftools - /usr/local/bin/bcftools [05:07:21] Found samtools - /usr/local/bin/samtools [05:07:21] Found java - /usr/local/bin/java [05:07:21] Found snpEff - /usr/local/bin/snpEff [05:07:21] Found samclip - /usr/local/bin/samclip [05:07:21] Found seqtk - /usr/local/bin/seqtk [05:07:21] Found parallel - /usr/local/bin/parallel [05:07:21] Found freebayes - /usr/local/bin/freebayes [05:07:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:07:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:07:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:07:21] Found vcfuniq - /usr/local/bin/vcfuniq [05:07:21] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:07:21] Found gzip - /bin/gzip [05:07:21] Found vt - /usr/local/bin/vt [05:07:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:07:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:07:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:07:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:07:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:07:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:07:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:07:22] Please supply a reference FASTA/GBK/EMBL file with --reference
2[05:07:30] This is snippy 4.6.0
Show full stderr[05:07:30] This is snippy 4.6.0 [05:07:30] Written by Torsten Seemann [05:07:30] Obtained from https://github.com/tseemann/snippy [05:07:30] Detected operating system: linux [05:07:30] Enabling bundled linux tools. [05:07:30] Found bwa - /usr/local/bin/bwa [05:07:30] Found bcftools - /usr/local/bin/bcftools [05:07:30] Found samtools - /usr/local/bin/samtools [05:07:30] Found java - /usr/local/bin/java [05:07:30] Found snpEff - /usr/local/bin/snpEff [05:07:30] Found samclip - /usr/local/bin/samclip [05:07:30] Found seqtk - /usr/local/bin/seqtk [05:07:30] Found parallel - /usr/local/bin/parallel [05:07:30] Found freebayes - /usr/local/bin/freebayes [05:07:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:07:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:07:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:07:30] Found vcfuniq - /usr/local/bin/vcfuniq [05:07:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:07:30] Found gzip - /bin/gzip [05:07:30] Found vt - /usr/local/bin/vt [05:07:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:07:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:07:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:07:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:07:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:07:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:07:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:07:32] Please supply a reference FASTA/GBK/EMBL file with --reference
2[05:07:36] This is snippy 4.6.0
Show full stderr[05:07:36] This is snippy 4.6.0 [05:07:36] Written by Torsten Seemann [05:07:36] Obtained from https://github.com/tseemann/snippy [05:07:36] Detected operating system: linux [05:07:36] Enabling bundled linux tools. [05:07:36] Found bwa - /usr/local/bin/bwa [05:07:36] Found bcftools - /usr/local/bin/bcftools [05:07:36] Found samtools - /usr/local/bin/samtools [05:07:36] Found java - /usr/local/bin/java [05:07:36] Found snpEff - /usr/local/bin/snpEff [05:07:36] Found samclip - /usr/local/bin/samclip [05:07:36] Found seqtk - /usr/local/bin/seqtk [05:07:36] Found parallel - /usr/local/bin/parallel [05:07:36] Found freebayes - /usr/local/bin/freebayes [05:07:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:07:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:07:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:07:36] Found vcfuniq - /usr/local/bin/vcfuniq [05:07:36] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:07:36] Found gzip - /bin/gzip [05:07:36] Found vt - /usr/local/bin/vt [05:07:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:07:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:07:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:07:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:07:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:07:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:07:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:07:37] Please supply a reference FASTA/GBK/EMBL file with --reference
2[05:07:06] This is snippy 4.6.0
Show full stderr[05:07:06] This is snippy 4.6.0 [05:07:06] Written by Torsten Seemann [05:07:06] Obtained from https://github.com/tseemann/snippy [05:07:06] Detected operating system: linux [05:07:06] Enabling bundled linux tools. [05:07:06] Found bwa - /usr/local/bin/bwa [05:07:06] Found bcftools - /usr/local/bin/bcftools [05:07:06] Found samtools - /usr/local/bin/samtools [05:07:06] Found java - /usr/local/bin/java [05:07:06] Found snpEff - /usr/local/bin/snpEff [05:07:06] Found samclip - /usr/local/bin/samclip [05:07:06] Found seqtk - /usr/local/bin/seqtk [05:07:06] Found parallel - /usr/local/bin/parallel [05:07:06] Found freebayes - /usr/local/bin/freebayes [05:07:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:07:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:07:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:07:06] Found vcfuniq - /usr/local/bin/vcfuniq [05:07:06] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:07:06] Found gzip - /bin/gzip [05:07:06] Found vt - /usr/local/bin/vt [05:07:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:07:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:07:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:07:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:07:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:07:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:07:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:07:07] Please supply a reference FASTA/GBK/EMBL file with --reference
2[05:07:51] This is snippy 4.6.0
Show full stderr[05:07:51] This is snippy 4.6.0 [05:07:51] Written by Torsten Seemann [05:07:51] Obtained from https://github.com/tseemann/snippy [05:07:51] Detected operating system: linux [05:07:51] Enabling bundled linux tools. [05:07:51] Found bwa - /usr/local/bin/bwa [05:07:51] Found bcftools - /usr/local/bin/bcftools [05:07:51] Found samtools - /usr/local/bin/samtools [05:07:51] Found java - /usr/local/bin/java [05:07:51] Found snpEff - /usr/local/bin/snpEff [05:07:51] Found samclip - /usr/local/bin/samclip [05:07:51] Found seqtk - /usr/local/bin/seqtk [05:07:51] Found parallel - /usr/local/bin/parallel [05:07:51] Found freebayes - /usr/local/bin/freebayes [05:07:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:07:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:07:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:07:51] Found vcfuniq - /usr/local/bin/vcfuniq [05:07:51] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:07:51] Found gzip - /bin/gzip [05:07:51] Found vt - /usr/local/bin/vt [05:07:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:07:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:07:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:07:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:07:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:07:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:07:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:07:52] Please supply a reference FASTA/GBK/EMBL file with --reference
2[05:07:57] This is snippy 4.6.0
Show full stderr[05:07:57] This is snippy 4.6.0 [05:07:57] Written by Torsten Seemann [05:07:57] Obtained from https://github.com/tseemann/snippy [05:07:57] Detected operating system: linux [05:07:57] Enabling bundled linux tools. [05:07:57] Found bwa - /usr/local/bin/bwa [05:07:57] Found bcftools - /usr/local/bin/bcftools [05:07:57] Found samtools - /usr/local/bin/samtools [05:07:57] Found java - /usr/local/bin/java [05:07:57] Found snpEff - /usr/local/bin/snpEff [05:07:57] Found samclip - /usr/local/bin/samclip [05:07:57] Found seqtk - /usr/local/bin/seqtk [05:07:57] Found parallel - /usr/local/bin/parallel [05:07:57] Found freebayes - /usr/local/bin/freebayes [05:07:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:07:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:07:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:07:57] Found vcfuniq - /usr/local/bin/vcfuniq [05:07:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:07:57] Found gzip - /bin/gzip [05:07:57] Found vt - /usr/local/bin/vt [05:07:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:07:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:07:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:07:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:07:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:07:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:07:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:07:58] Please supply a reference FASTA/GBK/EMBL file with --reference
2[05:08:12] This is snippy 4.6.0
Show full stderr[05:08:12] This is snippy 4.6.0 [05:08:12] Written by Torsten Seemann [05:08:12] Obtained from https://github.com/tseemann/snippy [05:08:12] Detected operating system: linux [05:08:12] Enabling bundled linux tools. [05:08:12] Found bwa - /usr/local/bin/bwa [05:08:12] Found bcftools - /usr/local/bin/bcftools [05:08:12] Found samtools - /usr/local/bin/samtools [05:08:12] Found java - /usr/local/bin/java [05:08:12] Found snpEff - /usr/local/bin/snpEff [05:08:12] Found samclip - /usr/local/bin/samclip [05:08:12] Found seqtk - /usr/local/bin/seqtk [05:08:12] Found parallel - /usr/local/bin/parallel [05:08:12] Found freebayes - /usr/local/bin/freebayes [05:08:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:08:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:08:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:08:12] Found vcfuniq - /usr/local/bin/vcfuniq [05:08:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:08:12] Found gzip - /bin/gzip [05:08:12] Found vt - /usr/local/bin/vt [05:08:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:08:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:08:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:08:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:08:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:08:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:08:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:08:13] Please supply a reference FASTA/GBK/EMBL file with --reference
2[05:08:39] This is snippy 4.6.0
Show full stderr[05:08:39] This is snippy 4.6.0 [05:08:39] Written by Torsten Seemann [05:08:39] Obtained from https://github.com/tseemann/snippy [05:08:39] Detected operating system: linux [05:08:39] Enabling bundled linux tools. [05:08:39] Found bwa - /usr/local/bin/bwa [05:08:39] Found bcftools - /usr/local/bin/bcftools [05:08:39] Found samtools - /usr/local/bin/samtools [05:08:39] Found java - /usr/local/bin/java [05:08:39] Found snpEff - /usr/local/bin/snpEff [05:08:39] Found samclip - /usr/local/bin/samclip [05:08:39] Found seqtk - /usr/local/bin/seqtk [05:08:39] Found parallel - /usr/local/bin/parallel [05:08:39] Found freebayes - /usr/local/bin/freebayes [05:08:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:08:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:08:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:08:39] Found vcfuniq - /usr/local/bin/vcfuniq [05:08:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:08:39] Found gzip - /bin/gzip [05:08:39] Found vt - /usr/local/bin/vt [05:08:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:08:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:08:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:08:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:08:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:08:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:08:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:08:40] Please supply a reference FASTA/GBK/EMBL file with --reference
2[05:09:09] This is snippy 4.6.0
Show full stderr[05:09:09] This is snippy 4.6.0 [05:09:09] Written by Torsten Seemann [05:09:09] Obtained from https://github.com/tseemann/snippy [05:09:09] Detected operating system: linux [05:09:09] Enabling bundled linux tools. [05:09:09] Found bwa - /usr/local/bin/bwa [05:09:09] Found bcftools - /usr/local/bin/bcftools [05:09:09] Found samtools - /usr/local/bin/samtools [05:09:09] Found java - /usr/local/bin/java [05:09:09] Found snpEff - /usr/local/bin/snpEff [05:09:09] Found samclip - /usr/local/bin/samclip [05:09:09] Found seqtk - /usr/local/bin/seqtk [05:09:09] Found parallel - /usr/local/bin/parallel [05:09:09] Found freebayes - /usr/local/bin/freebayes [05:09:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:09:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:09:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:09:09] Found vcfuniq - /usr/local/bin/vcfuniq [05:09:09] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:09:09] Found gzip - /bin/gzip [05:09:09] Found vt - /usr/local/bin/vt [05:09:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:09:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:09:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:09:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:09:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:09:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:09:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:09:10] Please supply a reference FASTA/GBK/EMBL file with --reference
2[05:09:24] This is snippy 4.6.0
Show full stderr[05:09:24] This is snippy 4.6.0 [05:09:24] Written by Torsten Seemann [05:09:24] Obtained from https://github.com/tseemann/snippy [05:09:24] Detected operating system: linux [05:09:24] Enabling bundled linux tools. [05:09:24] Found bwa - /usr/local/bin/bwa [05:09:24] Found bcftools - /usr/local/bin/bcftools [05:09:24] Found samtools - /usr/local/bin/samtools [05:09:24] Found java - /usr/local/bin/java [05:09:24] Found snpEff - /usr/local/bin/snpEff [05:09:24] Found samclip - /usr/local/bin/samclip [05:09:24] Found seqtk - /usr/local/bin/seqtk [05:09:24] Found parallel - /usr/local/bin/parallel [05:09:24] Found freebayes - /usr/local/bin/freebayes [05:09:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:09:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:09:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:09:24] Found vcfuniq - /usr/local/bin/vcfuniq [05:09:24] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:09:24] Found gzip - /bin/gzip [05:09:24] Found vt - /usr/local/bin/vt [05:09:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:09:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:09:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:09:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:09:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:09:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:09:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:09:25] Please supply a reference FASTA/GBK/EMBL file with --reference
2[05:09:39] This is snippy 4.6.0
Show full stderr[05:09:39] This is snippy 4.6.0 [05:09:39] Written by Torsten Seemann [05:09:39] Obtained from https://github.com/tseemann/snippy [05:09:39] Detected operating system: linux [05:09:39] Enabling bundled linux tools. [05:09:39] Found bwa - /usr/local/bin/bwa [05:09:39] Found bcftools - /usr/local/bin/bcftools [05:09:39] Found samtools - /usr/local/bin/samtools [05:09:39] Found java - /usr/local/bin/java [05:09:39] Found snpEff - /usr/local/bin/snpEff [05:09:39] Found samclip - /usr/local/bin/samclip [05:09:39] Found seqtk - /usr/local/bin/seqtk [05:09:39] Found parallel - /usr/local/bin/parallel [05:09:39] Found freebayes - /usr/local/bin/freebayes [05:09:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:09:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:09:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:09:39] Found vcfuniq - /usr/local/bin/vcfuniq [05:09:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:09:39] Found gzip - /bin/gzip [05:09:39] Found vt - /usr/local/bin/vt [05:09:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:09:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:09:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:09:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:09:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:09:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:09:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:09:40] Please supply a reference FASTA/GBK/EMBL file with --reference
2[05:03:02] This is snippy 4.6.0
Show full stderr[05:03:02] This is snippy 4.6.0 [05:03:02] Written by Torsten Seemann [05:03:02] Obtained from https://github.com/tseemann/snippy [05:03:02] Detected operating system: linux [05:03:02] Enabling bundled linux tools. [05:03:02] Found bwa - /usr/local/bin/bwa [05:03:02] Found bcftools - /usr/local/bin/bcftools [05:03:02] Found samtools - /usr/local/bin/samtools [05:03:02] Found java - /usr/local/bin/java [05:03:02] Found snpEff - /usr/local/bin/snpEff [05:03:02] Found samclip - /usr/local/bin/samclip [05:03:03] Found seqtk - /usr/local/bin/seqtk [05:03:03] Found parallel - /usr/local/bin/parallel [05:03:03] Found freebayes - /usr/local/bin/freebayes [05:03:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:03:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:03:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:03:03] Found vcfuniq - /usr/local/bin/vcfuniq [05:03:03] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:03:03] Found gzip - /bin/gzip [05:03:03] Found vt - /usr/local/bin/vt [05:03:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:03:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:03:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:03:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:03:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:03:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:03:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:03:03] Please supply a reference FASTA/GBK/EMBL file with --reference
2[05:04:50] This is snippy 4.6.0
Show full stderr[05:04:50] This is snippy 4.6.0 [05:04:50] Written by Torsten Seemann [05:04:50] Obtained from https://github.com/tseemann/snippy [05:04:50] Detected operating system: linux [05:04:50] Enabling bundled linux tools. [05:04:50] Found bwa - /usr/local/bin/bwa [05:04:50] Found bcftools - /usr/local/bin/bcftools [05:04:50] Found samtools - /usr/local/bin/samtools [05:04:50] Found java - /usr/local/bin/java [05:04:50] Found snpEff - /usr/local/bin/snpEff [05:04:50] Found samclip - /usr/local/bin/samclip [05:04:50] Found seqtk - /usr/local/bin/seqtk [05:04:50] Found parallel - /usr/local/bin/parallel [05:04:50] Found freebayes - /usr/local/bin/freebayes [05:04:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:04:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:04:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:04:50] Found vcfuniq - /usr/local/bin/vcfuniq [05:04:50] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:04:50] Found gzip - /bin/gzip [05:04:50] Found vt - /usr/local/bin/vt [05:04:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:04:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:04:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:04:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:04:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:04:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:04:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:04:51] Please supply a reference FASTA/GBK/EMBL file with --reference
2[05:09:48] This is snippy 4.6.0
Show full stderr[05:09:48] This is snippy 4.6.0 [05:09:48] Written by Torsten Seemann [05:09:48] Obtained from https://github.com/tseemann/snippy [05:09:48] Detected operating system: linux [05:09:48] Enabling bundled linux tools. [05:09:48] Found bwa - /usr/local/bin/bwa [05:09:48] Found bcftools - /usr/local/bin/bcftools [05:09:48] Found samtools - /usr/local/bin/samtools [05:09:48] Found java - /usr/local/bin/java [05:09:48] Found snpEff - /usr/local/bin/snpEff [05:09:48] Found samclip - /usr/local/bin/samclip [05:09:48] Found seqtk - /usr/local/bin/seqtk [05:09:48] Found parallel - /usr/local/bin/parallel [05:09:48] Found freebayes - /usr/local/bin/freebayes [05:09:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:09:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:09:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:09:48] Found vcfuniq - /usr/local/bin/vcfuniq [05:09:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:09:48] Found gzip - /bin/gzip [05:09:48] Found vt - /usr/local/bin/vt [05:09:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:09:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:09:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:09:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:09:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:09:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:09:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:09:49] Please supply a reference FASTA/GBK/EMBL file with --reference
2[05:09:54] This is snippy 4.6.0
Show full stderr[05:09:54] This is snippy 4.6.0 [05:09:54] Written by Torsten Seemann [05:09:54] Obtained from https://github.com/tseemann/snippy [05:09:54] Detected operating system: linux [05:09:54] Enabling bundled linux tools. [05:09:54] Found bwa - /usr/local/bin/bwa [05:09:54] Found bcftools - /usr/local/bin/bcftools [05:09:54] Found samtools - /usr/local/bin/samtools [05:09:54] Found java - /usr/local/bin/java [05:09:54] Found snpEff - /usr/local/bin/snpEff [05:09:54] Found samclip - /usr/local/bin/samclip [05:09:54] Found seqtk - /usr/local/bin/seqtk [05:09:54] Found parallel - /usr/local/bin/parallel [05:09:54] Found freebayes - /usr/local/bin/freebayes [05:09:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:09:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:09:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:09:54] Found vcfuniq - /usr/local/bin/vcfuniq [05:09:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:09:54] Found gzip - /bin/gzip [05:09:54] Found vt - /usr/local/bin/vt [05:09:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:09:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:09:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:09:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:09:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:09:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:09:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:09:55] Please supply a reference FASTA/GBK/EMBL file with --reference
2[05:10:09] This is snippy 4.6.0
Show full stderr[05:10:09] This is snippy 4.6.0 [05:10:09] Written by Torsten Seemann [05:10:09] Obtained from https://github.com/tseemann/snippy [05:10:09] Detected operating system: linux [05:10:09] Enabling bundled linux tools. [05:10:09] Found bwa - /usr/local/bin/bwa [05:10:09] Found bcftools - /usr/local/bin/bcftools [05:10:09] Found samtools - /usr/local/bin/samtools [05:10:09] Found java - /usr/local/bin/java [05:10:09] Found snpEff - /usr/local/bin/snpEff [05:10:09] Found samclip - /usr/local/bin/samclip [05:10:09] Found seqtk - /usr/local/bin/seqtk [05:10:09] Found parallel - /usr/local/bin/parallel [05:10:09] Found freebayes - /usr/local/bin/freebayes [05:10:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:10:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:10:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:10:09] Found vcfuniq - /usr/local/bin/vcfuniq [05:10:09] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:10:09] Found gzip - /bin/gzip [05:10:09] Found vt - /usr/local/bin/vt [05:10:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:10:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:10:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:10:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:10:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:10:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:10:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:10:10] Please supply a reference FASTA/GBK/EMBL file with --reference
2[05:10:27] This is snippy 4.6.0
Show full stderr[05:10:27] This is snippy 4.6.0 [05:10:27] Written by Torsten Seemann [05:10:27] Obtained from https://github.com/tseemann/snippy [05:10:27] Detected operating system: linux [05:10:27] Enabling bundled linux tools. [05:10:27] Found bwa - /usr/local/bin/bwa [05:10:27] Found bcftools - /usr/local/bin/bcftools [05:10:27] Found samtools - /usr/local/bin/samtools [05:10:27] Found java - /usr/local/bin/java [05:10:27] Found snpEff - /usr/local/bin/snpEff [05:10:27] Found samclip - /usr/local/bin/samclip [05:10:27] Found seqtk - /usr/local/bin/seqtk [05:10:27] Found parallel - /usr/local/bin/parallel [05:10:27] Found freebayes - /usr/local/bin/freebayes [05:10:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:10:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:10:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:10:27] Found vcfuniq - /usr/local/bin/vcfuniq [05:10:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:10:27] Found gzip - /bin/gzip [05:10:27] Found vt - /usr/local/bin/vt [05:10:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:10:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:10:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:10:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:10:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:10:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:10:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:10:28] Please supply a reference FASTA/GBK/EMBL file with --reference
2[05:05:03] This is snippy 4.6.0
Show full stderr[05:05:03] This is snippy 4.6.0 [05:05:03] Written by Torsten Seemann [05:05:03] Obtained from https://github.com/tseemann/snippy [05:05:03] Detected operating system: linux [05:05:03] Enabling bundled linux tools. [05:05:03] Found bwa - /usr/local/bin/bwa [05:05:03] Found bcftools - /usr/local/bin/bcftools [05:05:03] Found samtools - /usr/local/bin/samtools [05:05:03] Found java - /usr/local/bin/java [05:05:03] Found snpEff - /usr/local/bin/snpEff [05:05:03] Found samclip - /usr/local/bin/samclip [05:05:03] Found seqtk - /usr/local/bin/seqtk [05:05:03] Found parallel - /usr/local/bin/parallel [05:05:03] Found freebayes - /usr/local/bin/freebayes [05:05:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:05:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:05:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:05:03] Found vcfuniq - /usr/local/bin/vcfuniq [05:05:03] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:05:03] Found gzip - /bin/gzip [05:05:03] Found vt - /usr/local/bin/vt [05:05:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:05:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:05:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:05:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:05:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:05:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:05:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:05:04] Please supply a reference FASTA/GBK/EMBL file with --reference
2[05:05:39] This is snippy 4.6.0
Show full stderr[05:05:39] This is snippy 4.6.0 [05:05:39] Written by Torsten Seemann [05:05:39] Obtained from https://github.com/tseemann/snippy [05:05:39] Detected operating system: linux [05:05:39] Enabling bundled linux tools. [05:05:39] Found bwa - /usr/local/bin/bwa [05:05:39] Found bcftools - /usr/local/bin/bcftools [05:05:39] Found samtools - /usr/local/bin/samtools [05:05:39] Found java - /usr/local/bin/java [05:05:39] Found snpEff - /usr/local/bin/snpEff [05:05:39] Found samclip - /usr/local/bin/samclip [05:05:39] Found seqtk - /usr/local/bin/seqtk [05:05:39] Found parallel - /usr/local/bin/parallel [05:05:39] Found freebayes - /usr/local/bin/freebayes [05:05:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:05:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:05:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:05:39] Found vcfuniq - /usr/local/bin/vcfuniq [05:05:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:05:39] Found gzip - /bin/gzip [05:05:39] Found vt - /usr/local/bin/vt [05:05:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:05:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:05:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:05:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:05:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:05:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:05:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:05:41] Please supply a reference FASTA/GBK/EMBL file with --reference
2[05:06:14] This is snippy 4.6.0
Show full stderr[05:06:14] This is snippy 4.6.0 [05:06:14] Written by Torsten Seemann [05:06:14] Obtained from https://github.com/tseemann/snippy [05:06:14] Detected operating system: linux [05:06:14] Enabling bundled linux tools. [05:06:14] Found bwa - /usr/local/bin/bwa [05:06:14] Found bcftools - /usr/local/bin/bcftools [05:06:14] Found samtools - /usr/local/bin/samtools [05:06:14] Found java - /usr/local/bin/java [05:06:14] Found snpEff - /usr/local/bin/snpEff [05:06:14] Found samclip - /usr/local/bin/samclip [05:06:14] Found seqtk - /usr/local/bin/seqtk [05:06:14] Found parallel - /usr/local/bin/parallel [05:06:14] Found freebayes - /usr/local/bin/freebayes [05:06:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:06:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:06:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:06:14] Found vcfuniq - /usr/local/bin/vcfuniq [05:06:14] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:06:14] Found gzip - /bin/gzip [05:06:14] Found vt - /usr/local/bin/vt [05:06:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:06:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:06:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:06:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:06:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:06:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:06:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:06:15] Please supply a reference FASTA/GBK/EMBL file with --reference
2[05:06:33] This is snippy 4.6.0
Show full stderr[05:06:33] This is snippy 4.6.0 [05:06:33] Written by Torsten Seemann [05:06:33] Obtained from https://github.com/tseemann/snippy [05:06:33] Detected operating system: linux [05:06:33] Enabling bundled linux tools. [05:06:33] Found bwa - /usr/local/bin/bwa [05:06:33] Found bcftools - /usr/local/bin/bcftools [05:06:33] Found samtools - /usr/local/bin/samtools [05:06:33] Found java - /usr/local/bin/java [05:06:33] Found snpEff - /usr/local/bin/snpEff [05:06:33] Found samclip - /usr/local/bin/samclip [05:06:33] Found seqtk - /usr/local/bin/seqtk [05:06:33] Found parallel - /usr/local/bin/parallel [05:06:33] Found freebayes - /usr/local/bin/freebayes [05:06:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:06:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:06:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:06:33] Found vcfuniq - /usr/local/bin/vcfuniq [05:06:33] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:06:33] Found gzip - /bin/gzip [05:06:33] Found vt - /usr/local/bin/vt [05:06:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:06:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:06:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:06:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:06:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:06:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:06:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:06:34] Please supply a reference FASTA/GBK/EMBL file with --reference
2[05:10:24] This is snippy 4.6.0
Show full stderr[05:10:24] This is snippy 4.6.0 [05:10:24] Written by Torsten Seemann [05:10:24] Obtained from https://github.com/tseemann/snippy [05:10:24] Detected operating system: linux [05:10:24] Enabling bundled linux tools. [05:10:24] Found bwa - /usr/local/bin/bwa [05:10:24] Found bcftools - /usr/local/bin/bcftools [05:10:24] Found samtools - /usr/local/bin/samtools [05:10:24] Found java - /usr/local/bin/java [05:10:24] Found snpEff - /usr/local/bin/snpEff [05:10:24] Found samclip - /usr/local/bin/samclip [05:10:24] Found seqtk - /usr/local/bin/seqtk [05:10:24] Found parallel - /usr/local/bin/parallel [05:10:24] Found freebayes - /usr/local/bin/freebayes [05:10:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:10:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:10:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:10:24] Found vcfuniq - /usr/local/bin/vcfuniq [05:10:24] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:10:24] Found gzip - /bin/gzip [05:10:24] Found vt - /usr/local/bin/vt [05:10:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:10:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:10:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:10:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:10:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:10:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:10:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:10:25] Please supply a reference FASTA/GBK/EMBL file with --reference
2[05:08:09] This is snippy 4.6.0
Show full stderr[05:08:09] This is snippy 4.6.0 [05:08:09] Written by Torsten Seemann [05:08:09] Obtained from https://github.com/tseemann/snippy [05:08:09] Detected operating system: linux [05:08:09] Enabling bundled linux tools. [05:08:09] Found bwa - /usr/local/bin/bwa [05:08:09] Found bcftools - /usr/local/bin/bcftools [05:08:09] Found samtools - /usr/local/bin/samtools [05:08:09] Found java - /usr/local/bin/java [05:08:09] Found snpEff - /usr/local/bin/snpEff [05:08:09] Found samclip - /usr/local/bin/samclip [05:08:09] Found seqtk - /usr/local/bin/seqtk [05:08:09] Found parallel - /usr/local/bin/parallel [05:08:09] Found freebayes - /usr/local/bin/freebayes [05:08:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:08:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:08:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:08:09] Found vcfuniq - /usr/local/bin/vcfuniq [05:08:09] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:08:09] Found gzip - /bin/gzip [05:08:09] Found vt - /usr/local/bin/vt [05:08:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:08:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:08:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:08:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:08:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:08:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:08:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:08:10] Please supply a reference FASTA/GBK/EMBL file with --reference
2[05:08:42] This is snippy 4.6.0
Show full stderr[05:08:42] This is snippy 4.6.0 [05:08:42] Written by Torsten Seemann [05:08:42] Obtained from https://github.com/tseemann/snippy [05:08:42] Detected operating system: linux [05:08:42] Enabling bundled linux tools. [05:08:42] Found bwa - /usr/local/bin/bwa [05:08:42] Found bcftools - /usr/local/bin/bcftools [05:08:42] Found samtools - /usr/local/bin/samtools [05:08:42] Found java - /usr/local/bin/java [05:08:42] Found snpEff - /usr/local/bin/snpEff [05:08:42] Found samclip - /usr/local/bin/samclip [05:08:42] Found seqtk - /usr/local/bin/seqtk [05:08:42] Found parallel - /usr/local/bin/parallel [05:08:42] Found freebayes - /usr/local/bin/freebayes [05:08:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:08:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:08:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:08:42] Found vcfuniq - /usr/local/bin/vcfuniq [05:08:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:08:42] Found gzip - /bin/gzip [05:08:42] Found vt - /usr/local/bin/vt [05:08:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:08:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:08:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:08:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:08:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:08:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:08:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:08:43] Please supply a reference FASTA/GBK/EMBL file with --reference
2[05:11:30] This is snippy 4.6.0
Show full stderr[05:11:30] This is snippy 4.6.0 [05:11:30] Written by Torsten Seemann [05:11:30] Obtained from https://github.com/tseemann/snippy [05:11:30] Detected operating system: linux [05:11:30] Enabling bundled linux tools. [05:11:30] Found bwa - /usr/local/bin/bwa [05:11:30] Found bcftools - /usr/local/bin/bcftools [05:11:30] Found samtools - /usr/local/bin/samtools [05:11:30] Found java - /usr/local/bin/java [05:11:30] Found snpEff - /usr/local/bin/snpEff [05:11:30] Found samclip - /usr/local/bin/samclip [05:11:30] Found seqtk - /usr/local/bin/seqtk [05:11:30] Found parallel - /usr/local/bin/parallel [05:11:30] Found freebayes - /usr/local/bin/freebayes [05:11:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:11:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:11:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:11:30] Found vcfuniq - /usr/local/bin/vcfuniq [05:11:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:11:30] Found gzip - /bin/gzip [05:11:30] Found vt - /usr/local/bin/vt [05:11:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:11:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:11:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:11:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:11:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:11:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:11:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:11:32] Please supply a reference FASTA/GBK/EMBL file with --reference
2[05:11:42] This is snippy 4.6.0
Show full stderr[05:11:42] This is snippy 4.6.0 [05:11:42] Written by Torsten Seemann [05:11:42] Obtained from https://github.com/tseemann/snippy [05:11:42] Detected operating system: linux [05:11:42] Enabling bundled linux tools. [05:11:42] Found bwa - /usr/local/bin/bwa [05:11:42] Found bcftools - /usr/local/bin/bcftools [05:11:42] Found samtools - /usr/local/bin/samtools [05:11:42] Found java - /usr/local/bin/java [05:11:42] Found snpEff - /usr/local/bin/snpEff [05:11:42] Found samclip - /usr/local/bin/samclip [05:11:42] Found seqtk - /usr/local/bin/seqtk [05:11:42] Found parallel - /usr/local/bin/parallel [05:11:42] Found freebayes - /usr/local/bin/freebayes [05:11:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:11:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:11:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:11:42] Found vcfuniq - /usr/local/bin/vcfuniq [05:11:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:11:42] Found gzip - /bin/gzip [05:11:42] Found vt - /usr/local/bin/vt [05:11:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:11:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:11:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:11:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:11:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:11:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:11:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:11:43] Please supply a reference FASTA/GBK/EMBL file with --reference
2[05:08:57] This is snippy 4.6.0
Show full stderr[05:08:57] This is snippy 4.6.0 [05:08:57] Written by Torsten Seemann [05:08:57] Obtained from https://github.com/tseemann/snippy [05:08:57] Detected operating system: linux [05:08:57] Enabling bundled linux tools. [05:08:57] Found bwa - /usr/local/bin/bwa [05:08:57] Found bcftools - /usr/local/bin/bcftools [05:08:57] Found samtools - /usr/local/bin/samtools [05:08:57] Found java - /usr/local/bin/java [05:08:57] Found snpEff - /usr/local/bin/snpEff [05:08:57] Found samclip - /usr/local/bin/samclip [05:08:57] Found seqtk - /usr/local/bin/seqtk [05:08:57] Found parallel - /usr/local/bin/parallel [05:08:57] Found freebayes - /usr/local/bin/freebayes [05:08:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:08:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:08:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:08:57] Found vcfuniq - /usr/local/bin/vcfuniq [05:08:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:08:57] Found gzip - /bin/gzip [05:08:57] Found vt - /usr/local/bin/vt [05:08:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:08:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:08:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:08:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:08:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:08:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:08:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:08:58] Please supply a reference FASTA/GBK/EMBL file with --reference
2[03:39:33] This is snippy 4.6.0
Show full stderr[03:39:33] This is snippy 4.6.0 [03:39:33] Written by Torsten Seemann [03:39:33] Obtained from https://github.com/tseemann/snippy [03:39:33] Detected operating system: linux [03:39:33] Enabling bundled linux tools. [03:39:33] Found bwa - /usr/local/bin/bwa [03:39:33] Found bcftools - /usr/local/bin/bcftools [03:39:33] Found samtools - /usr/local/bin/samtools [03:39:33] Found java - /usr/local/bin/java [03:39:33] Found snpEff - /usr/local/bin/snpEff [03:39:33] Found samclip - /usr/local/bin/samclip [03:39:33] Found seqtk - /usr/local/bin/seqtk [03:39:33] Found parallel - /usr/local/bin/parallel [03:39:33] Found freebayes - /usr/local/bin/freebayes [03:39:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:39:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:39:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:39:33] Found vcfuniq - /usr/local/bin/vcfuniq [03:39:33] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:39:33] Found gzip - /bin/gzip [03:39:33] Found vt - /usr/local/bin/vt [03:39:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:39:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:39:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:39:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:39:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:39:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:39:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:39:34] Please supply a reference FASTA/GBK/EMBL file with --reference
2[03:40:34] This is snippy 4.6.0
Show full stderr[03:40:34] This is snippy 4.6.0 [03:40:34] Written by Torsten Seemann [03:40:34] Obtained from https://github.com/tseemann/snippy [03:40:34] Detected operating system: linux [03:40:34] Enabling bundled linux tools. [03:40:34] Found bwa - /usr/local/bin/bwa [03:40:34] Found bcftools - /usr/local/bin/bcftools [03:40:34] Found samtools - /usr/local/bin/samtools [03:40:34] Found java - /usr/local/bin/java [03:40:34] Found snpEff - /usr/local/bin/snpEff [03:40:34] Found samclip - /usr/local/bin/samclip [03:40:34] Found seqtk - /usr/local/bin/seqtk [03:40:34] Found parallel - /usr/local/bin/parallel [03:40:34] Found freebayes - /usr/local/bin/freebayes [03:40:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:40:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:40:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:40:34] Found vcfuniq - /usr/local/bin/vcfuniq [03:40:34] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:40:34] Found gzip - /bin/gzip [03:40:34] Found vt - /usr/local/bin/vt [03:40:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:40:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:40:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:40:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:40:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:40:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:40:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:40:35] Please supply a reference FASTA/GBK/EMBL file with --reference
2[03:41:27] This is snippy 4.6.0
Show full stderr[03:41:27] This is snippy 4.6.0 [03:41:27] Written by Torsten Seemann [03:41:27] Obtained from https://github.com/tseemann/snippy [03:41:27] Detected operating system: linux [03:41:27] Enabling bundled linux tools. [03:41:27] Found bwa - /usr/local/bin/bwa [03:41:27] Found bcftools - /usr/local/bin/bcftools [03:41:27] Found samtools - /usr/local/bin/samtools [03:41:27] Found java - /usr/local/bin/java [03:41:27] Found snpEff - /usr/local/bin/snpEff [03:41:27] Found samclip - /usr/local/bin/samclip [03:41:27] Found seqtk - /usr/local/bin/seqtk [03:41:27] Found parallel - /usr/local/bin/parallel [03:41:27] Found freebayes - /usr/local/bin/freebayes [03:41:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:41:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:41:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:41:27] Found vcfuniq - /usr/local/bin/vcfuniq [03:41:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:41:27] Found gzip - /bin/gzip [03:41:27] Found vt - /usr/local/bin/vt [03:41:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:41:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:41:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:41:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:41:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:41:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:41:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:41:28] Please supply a reference FASTA/GBK/EMBL file with --reference
2[03:40:49] This is snippy 4.6.0
Show full stderr[03:40:49] This is snippy 4.6.0 [03:40:49] Written by Torsten Seemann [03:40:49] Obtained from https://github.com/tseemann/snippy [03:40:49] Detected operating system: linux [03:40:49] Enabling bundled linux tools. [03:40:49] Found bwa - /usr/local/bin/bwa [03:40:49] Found bcftools - /usr/local/bin/bcftools [03:40:49] Found samtools - /usr/local/bin/samtools [03:40:49] Found java - /usr/local/bin/java [03:40:49] Found snpEff - /usr/local/bin/snpEff [03:40:49] Found samclip - /usr/local/bin/samclip [03:40:49] Found seqtk - /usr/local/bin/seqtk [03:40:49] Found parallel - /usr/local/bin/parallel [03:40:49] Found freebayes - /usr/local/bin/freebayes [03:40:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:40:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:40:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:40:49] Found vcfuniq - /usr/local/bin/vcfuniq [03:40:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:40:49] Found gzip - /bin/gzip [03:40:49] Found vt - /usr/local/bin/vt [03:40:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:40:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:40:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:40:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:40:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:40:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:40:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:40:50] Please supply a reference FASTA/GBK/EMBL file with --reference
2[03:41:00] This is snippy 4.6.0
Show full stderr[03:41:00] This is snippy 4.6.0 [03:41:00] Written by Torsten Seemann [03:41:00] Obtained from https://github.com/tseemann/snippy [03:41:00] Detected operating system: linux [03:41:00] Enabling bundled linux tools. [03:41:00] Found bwa - /usr/local/bin/bwa [03:41:00] Found bcftools - /usr/local/bin/bcftools [03:41:00] Found samtools - /usr/local/bin/samtools [03:41:00] Found java - /usr/local/bin/java [03:41:00] Found snpEff - /usr/local/bin/snpEff [03:41:00] Found samclip - /usr/local/bin/samclip [03:41:00] Found seqtk - /usr/local/bin/seqtk [03:41:00] Found parallel - /usr/local/bin/parallel [03:41:00] Found freebayes - /usr/local/bin/freebayes [03:41:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:41:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:41:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:41:00] Found vcfuniq - /usr/local/bin/vcfuniq [03:41:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:41:00] Found gzip - /bin/gzip [03:41:00] Found vt - /usr/local/bin/vt [03:41:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:41:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:41:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:41:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:41:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:41:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:41:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:41:01] Please supply a reference FASTA/GBK/EMBL file with --reference
2[03:42:00] This is snippy 4.6.0
Show full stderr[03:42:00] This is snippy 4.6.0 [03:42:00] Written by Torsten Seemann [03:42:00] Obtained from https://github.com/tseemann/snippy [03:42:00] Detected operating system: linux [03:42:00] Enabling bundled linux tools. [03:42:00] Found bwa - /usr/local/bin/bwa [03:42:00] Found bcftools - /usr/local/bin/bcftools [03:42:00] Found samtools - /usr/local/bin/samtools [03:42:00] Found java - /usr/local/bin/java [03:42:00] Found snpEff - /usr/local/bin/snpEff [03:42:00] Found samclip - /usr/local/bin/samclip [03:42:00] Found seqtk - /usr/local/bin/seqtk [03:42:00] Found parallel - /usr/local/bin/parallel [03:42:00] Found freebayes - /usr/local/bin/freebayes [03:42:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:42:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:42:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:42:00] Found vcfuniq - /usr/local/bin/vcfuniq [03:42:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:42:00] Found gzip - /bin/gzip [03:42:00] Found vt - /usr/local/bin/vt [03:42:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:42:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:42:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:42:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:42:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:42:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:42:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:42:01] Please supply a reference FASTA/GBK/EMBL file with --reference
2[03:42:16] This is snippy 4.6.0
Show full stderr[03:42:16] This is snippy 4.6.0 [03:42:16] Written by Torsten Seemann [03:42:16] Obtained from https://github.com/tseemann/snippy [03:42:16] Detected operating system: linux [03:42:16] Enabling bundled linux tools. [03:42:16] Found bwa - /usr/local/bin/bwa [03:42:16] Found bcftools - /usr/local/bin/bcftools [03:42:16] Found samtools - /usr/local/bin/samtools [03:42:16] Found java - /usr/local/bin/java [03:42:16] Found snpEff - /usr/local/bin/snpEff [03:42:16] Found samclip - /usr/local/bin/samclip [03:42:16] Found seqtk - /usr/local/bin/seqtk [03:42:16] Found parallel - /usr/local/bin/parallel [03:42:16] Found freebayes - /usr/local/bin/freebayes [03:42:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:42:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:42:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:42:16] Found vcfuniq - /usr/local/bin/vcfuniq [03:42:16] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:42:16] Found gzip - /bin/gzip [03:42:16] Found vt - /usr/local/bin/vt [03:42:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:42:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:42:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:42:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:42:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:42:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:42:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:42:17] Please supply a reference FASTA/GBK/EMBL file with --reference
2[03:43:10] This is snippy 4.6.0
Show full stderr[03:43:10] This is snippy 4.6.0 [03:43:10] Written by Torsten Seemann [03:43:10] Obtained from https://github.com/tseemann/snippy [03:43:10] Detected operating system: linux [03:43:10] Enabling bundled linux tools. [03:43:10] Found bwa - /usr/local/bin/bwa [03:43:10] Found bcftools - /usr/local/bin/bcftools [03:43:10] Found samtools - /usr/local/bin/samtools [03:43:10] Found java - /usr/local/bin/java [03:43:10] Found snpEff - /usr/local/bin/snpEff [03:43:10] Found samclip - /usr/local/bin/samclip [03:43:10] Found seqtk - /usr/local/bin/seqtk [03:43:10] Found parallel - /usr/local/bin/parallel [03:43:10] Found freebayes - /usr/local/bin/freebayes [03:43:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:43:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:43:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:43:10] Found vcfuniq - /usr/local/bin/vcfuniq [03:43:10] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:43:10] Found gzip - /bin/gzip [03:43:10] Found vt - /usr/local/bin/vt [03:43:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:43:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:43:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:43:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:43:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:43:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:43:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:43:11] Please supply a reference FASTA/GBK/EMBL file with --reference
2[03:43:28] This is snippy 4.6.0
Show full stderr[03:43:28] This is snippy 4.6.0 [03:43:28] Written by Torsten Seemann [03:43:28] Obtained from https://github.com/tseemann/snippy [03:43:28] Detected operating system: linux [03:43:28] Enabling bundled linux tools. [03:43:28] Found bwa - /usr/local/bin/bwa [03:43:28] Found bcftools - /usr/local/bin/bcftools [03:43:28] Found samtools - /usr/local/bin/samtools [03:43:28] Found java - /usr/local/bin/java [03:43:28] Found snpEff - /usr/local/bin/snpEff [03:43:28] Found samclip - /usr/local/bin/samclip [03:43:28] Found seqtk - /usr/local/bin/seqtk [03:43:28] Found parallel - /usr/local/bin/parallel [03:43:28] Found freebayes - /usr/local/bin/freebayes [03:43:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:43:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:43:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:43:28] Found vcfuniq - /usr/local/bin/vcfuniq [03:43:28] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:43:28] Found gzip - /bin/gzip [03:43:28] Found vt - /usr/local/bin/vt [03:43:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:43:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:43:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:43:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:43:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:43:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:43:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:43:29] Please supply a reference FASTA/GBK/EMBL file with --reference
2[03:43:43] This is snippy 4.6.0
Show full stderr[03:43:43] This is snippy 4.6.0 [03:43:43] Written by Torsten Seemann [03:43:43] Obtained from https://github.com/tseemann/snippy [03:43:43] Detected operating system: linux [03:43:43] Enabling bundled linux tools. [03:43:43] Found bwa - /usr/local/bin/bwa [03:43:43] Found bcftools - /usr/local/bin/bcftools [03:43:43] Found samtools - /usr/local/bin/samtools [03:43:43] Found java - /usr/local/bin/java [03:43:43] Found snpEff - /usr/local/bin/snpEff [03:43:43] Found samclip - /usr/local/bin/samclip [03:43:43] Found seqtk - /usr/local/bin/seqtk [03:43:43] Found parallel - /usr/local/bin/parallel [03:43:43] Found freebayes - /usr/local/bin/freebayes [03:43:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:43:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:43:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:43:43] Found vcfuniq - /usr/local/bin/vcfuniq [03:43:43] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:43:43] Found gzip - /bin/gzip [03:43:43] Found vt - /usr/local/bin/vt [03:43:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:43:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:43:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:43:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:43:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:43:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:43:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:43:44] Please supply a reference FASTA/GBK/EMBL file with --reference
2[03:42:10] This is snippy 4.6.0
Show full stderr[03:42:10] This is snippy 4.6.0 [03:42:10] Written by Torsten Seemann [03:42:10] Obtained from https://github.com/tseemann/snippy [03:42:10] Detected operating system: linux [03:42:10] Enabling bundled linux tools. [03:42:10] Found bwa - /usr/local/bin/bwa [03:42:10] Found bcftools - /usr/local/bin/bcftools [03:42:10] Found samtools - /usr/local/bin/samtools [03:42:10] Found java - /usr/local/bin/java [03:42:10] Found snpEff - /usr/local/bin/snpEff [03:42:10] Found samclip - /usr/local/bin/samclip [03:42:10] Found seqtk - /usr/local/bin/seqtk [03:42:10] Found parallel - /usr/local/bin/parallel [03:42:10] Found freebayes - /usr/local/bin/freebayes [03:42:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:42:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:42:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:42:10] Found vcfuniq - /usr/local/bin/vcfuniq [03:42:10] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:42:10] Found gzip - /bin/gzip [03:42:10] Found vt - /usr/local/bin/vt [03:42:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:42:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:42:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:42:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:42:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:42:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:42:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:42:11] Please supply a reference FASTA/GBK/EMBL file with --reference
2[03:43:58] This is snippy 4.6.0
Show full stderr[03:43:58] This is snippy 4.6.0 [03:43:58] Written by Torsten Seemann [03:43:58] Obtained from https://github.com/tseemann/snippy [03:43:58] Detected operating system: linux [03:43:58] Enabling bundled linux tools. [03:43:58] Found bwa - /usr/local/bin/bwa [03:43:58] Found bcftools - /usr/local/bin/bcftools [03:43:58] Found samtools - /usr/local/bin/samtools [03:43:58] Found java - /usr/local/bin/java [03:43:58] Found snpEff - /usr/local/bin/snpEff [03:43:58] Found samclip - /usr/local/bin/samclip [03:43:58] Found seqtk - /usr/local/bin/seqtk [03:43:58] Found parallel - /usr/local/bin/parallel [03:43:58] Found freebayes - /usr/local/bin/freebayes [03:43:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:43:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:43:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:43:58] Found vcfuniq - /usr/local/bin/vcfuniq [03:43:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:43:58] Found gzip - /bin/gzip [03:43:58] Found vt - /usr/local/bin/vt [03:43:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:43:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:43:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:43:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:43:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:43:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:43:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:43:59] Please supply a reference FASTA/GBK/EMBL file with --reference
2[03:44:13] This is snippy 4.6.0
Show full stderr[03:44:13] This is snippy 4.6.0 [03:44:13] Written by Torsten Seemann [03:44:13] Obtained from https://github.com/tseemann/snippy [03:44:13] Detected operating system: linux [03:44:13] Enabling bundled linux tools. [03:44:13] Found bwa - /usr/local/bin/bwa [03:44:13] Found bcftools - /usr/local/bin/bcftools [03:44:13] Found samtools - /usr/local/bin/samtools [03:44:13] Found java - /usr/local/bin/java [03:44:13] Found snpEff - /usr/local/bin/snpEff [03:44:13] Found samclip - /usr/local/bin/samclip [03:44:13] Found seqtk - /usr/local/bin/seqtk [03:44:13] Found parallel - /usr/local/bin/parallel [03:44:13] Found freebayes - /usr/local/bin/freebayes [03:44:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:44:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:44:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:44:13] Found vcfuniq - /usr/local/bin/vcfuniq [03:44:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:44:13] Found gzip - /bin/gzip [03:44:13] Found vt - /usr/local/bin/vt [03:44:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:44:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:44:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:44:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:44:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:44:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:44:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:44:14] Please supply a reference FASTA/GBK/EMBL file with --reference
2[05:57:56] This is snippy 4.6.0
Show full stderr[05:57:56] This is snippy 4.6.0 [05:57:56] Written by Torsten Seemann [05:57:56] Obtained from https://github.com/tseemann/snippy [05:57:56] Detected operating system: linux [05:57:56] Enabling bundled linux tools. [05:57:56] Found bwa - /usr/local/bin/bwa [05:57:56] Found bcftools - /usr/local/bin/bcftools [05:57:56] Found samtools - /usr/local/bin/samtools [05:57:56] Found java - /usr/local/bin/java [05:57:56] Found snpEff - /usr/local/bin/snpEff [05:57:56] Found samclip - /usr/local/bin/samclip [05:57:56] Found seqtk - /usr/local/bin/seqtk [05:57:56] Found parallel - /usr/local/bin/parallel [05:57:56] Found freebayes - /usr/local/bin/freebayes [05:57:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:57:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:57:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:57:57] Found vcfuniq - /usr/local/bin/vcfuniq [05:57:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:57:57] Found gzip - /bin/gzip [05:57:57] Found vt - /usr/local/bin/vt [05:57:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:57:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:57:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:57:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:57:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:57:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:57:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:57:58] Using reference: /cvmfs/data.galaxyproject.org/byhand/microbes/eschColi_APEC_O1/seq/eschColi_APEC_O1.fa [05:57:58] Treating reference as 'fasta' format. [05:57:58] Will use 1 CPU cores. [05:57:58] Using read file: /corral4/main/objects/c/5/6/dataset_c562894c-07c6-4167-b0aa-6a642b1bae17.dat [05:57:58] Creating folder: Resistance_28_fasta [05:57:58] Changing working directory: Resistance_28_fasta [05:57:58] Creating reference folder: reference [05:57:58] Extracting FASTA and GFF from reference. [05:57:58] Wrote 3 sequences to ref.fa [05:57:58] Wrote 0 features to ref.gff [05:57:58] Shredding /corral4/main/objects/c/5/6/dataset_c562894c-07c6-4167-b0aa-6a642b1bae17.dat into pseudo-reads [05:58:05] Wrote 439720 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [05:58:05] Freebayes will process 1 chunks of 5589314 bp, 1 chunks at a time. [05:58:05] Using BAM RG (Read Group) ID: Resistance_28_fasta [05:58:05] Running: samtools faidx reference/ref.fa 2>> snps.log [05:58:05] Running: bwa index reference/ref.fa 2>> snps.log [05:58:11] Error running command, check Resistance_28_fasta/snps.log
2[05:58:13] This is snippy 4.6.0
Show full stderr[05:58:13] This is snippy 4.6.0 [05:58:13] Written by Torsten Seemann [05:58:13] Obtained from https://github.com/tseemann/snippy [05:58:13] Detected operating system: linux [05:58:13] Enabling bundled linux tools. [05:58:13] Found bwa - /usr/local/bin/bwa [05:58:13] Found bcftools - /usr/local/bin/bcftools [05:58:13] Found samtools - /usr/local/bin/samtools [05:58:13] Found java - /usr/local/bin/java [05:58:13] Found snpEff - /usr/local/bin/snpEff [05:58:13] Found samclip - /usr/local/bin/samclip [05:58:13] Found seqtk - /usr/local/bin/seqtk [05:58:13] Found parallel - /usr/local/bin/parallel [05:58:13] Found freebayes - /usr/local/bin/freebayes [05:58:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:58:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:58:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:58:13] Found vcfuniq - /usr/local/bin/vcfuniq [05:58:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:58:13] Found gzip - /bin/gzip [05:58:13] Found vt - /usr/local/bin/vt [05:58:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:58:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:58:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:58:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:58:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:58:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:58:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:58:14] Using reference: /cvmfs/data.galaxyproject.org/byhand/microbes/eschColi_APEC_O1/seq/eschColi_APEC_O1.fa [05:58:14] Treating reference as 'fasta' format. [05:58:14] Will use 1 CPU cores. [05:58:14] Using read file: /corral4/main/objects/7/3/5/dataset_735d5f4d-4c45-4594-b696-4f2376c449f0.dat [05:58:14] Creating folder: Resistance_63_fasta [05:58:14] Changing working directory: Resistance_63_fasta [05:58:14] Creating reference folder: reference [05:58:14] Extracting FASTA and GFF from reference. [05:58:15] Wrote 3 sequences to ref.fa [05:58:15] Wrote 0 features to ref.gff [05:58:15] Shredding /corral4/main/objects/7/3/5/dataset_735d5f4d-4c45-4594-b696-4f2376c449f0.dat into pseudo-reads [05:58:19] Wrote 388254 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [05:58:19] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time. [05:58:19] Using BAM RG (Read Group) ID: Resistance_63_fasta [05:58:19] Running: samtools faidx reference/ref.fa 2>> snps.log [05:58:19] Error running command, check Resistance_63_fasta/snps.log
2[05:58:14] This is snippy 4.6.0
Show full stderr[05:58:14] This is snippy 4.6.0 [05:58:14] Written by Torsten Seemann [05:58:14] Obtained from https://github.com/tseemann/snippy [05:58:14] Detected operating system: linux [05:58:14] Enabling bundled linux tools. [05:58:14] Found bwa - /usr/local/bin/bwa [05:58:14] Found bcftools - /usr/local/bin/bcftools [05:58:14] Found samtools - /usr/local/bin/samtools [05:58:14] Found java - /usr/local/bin/java [05:58:14] Found snpEff - /usr/local/bin/snpEff [05:58:14] Found samclip - /usr/local/bin/samclip [05:58:14] Found seqtk - /usr/local/bin/seqtk [05:58:14] Found parallel - /usr/local/bin/parallel [05:58:14] Found freebayes - /usr/local/bin/freebayes [05:58:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:58:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:58:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:58:14] Found vcfuniq - /usr/local/bin/vcfuniq [05:58:14] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:58:14] Found gzip - /bin/gzip [05:58:14] Found vt - /usr/local/bin/vt [05:58:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:58:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:58:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:58:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:58:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:58:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:58:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:58:16] Using reference: /cvmfs/data.galaxyproject.org/byhand/microbes/eschColi_APEC_O1/seq/eschColi_APEC_O1.fa [05:58:16] Treating reference as 'fasta' format. [05:58:16] Will use 1 CPU cores. [05:58:16] Using read file: /corral4/main/objects/e/4/e/dataset_e4ec5ef2-d531-4a2f-bf23-97ecb3a510b7.dat [05:58:16] Creating folder: Resistance_64_fasta [05:58:16] Changing working directory: Resistance_64_fasta [05:58:16] Creating reference folder: reference [05:58:16] Extracting FASTA and GFF from reference. [05:58:16] Wrote 3 sequences to ref.fa [05:58:16] Wrote 0 features to ref.gff [05:58:16] Shredding /corral4/main/objects/e/4/e/dataset_e4ec5ef2-d531-4a2f-bf23-97ecb3a510b7.dat into pseudo-reads [05:58:20] Wrote 392922 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [05:58:20] Freebayes will process 1 chunks of 5589314 bp, 1 chunks at a time. [05:58:20] Using BAM RG (Read Group) ID: Resistance_64_fasta [05:58:20] Running: samtools faidx reference/ref.fa 2>> snps.log [05:58:20] Error running command, check Resistance_64_fasta/snps.log
2[05:59:34] This is snippy 4.6.0
Show full stderr[05:59:34] This is snippy 4.6.0 [05:59:34] Written by Torsten Seemann [05:59:34] Obtained from https://github.com/tseemann/snippy [05:59:34] Detected operating system: linux [05:59:34] Enabling bundled linux tools. [05:59:34] Found bwa - /usr/local/bin/bwa [05:59:34] Found bcftools - /usr/local/bin/bcftools [05:59:34] Found samtools - /usr/local/bin/samtools [05:59:34] Found java - /usr/local/bin/java [05:59:34] Found snpEff - /usr/local/bin/snpEff [05:59:34] Found samclip - /usr/local/bin/samclip [05:59:34] Found seqtk - /usr/local/bin/seqtk [05:59:34] Found parallel - /usr/local/bin/parallel [05:59:34] Found freebayes - /usr/local/bin/freebayes [05:59:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:59:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:59:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:59:34] Found vcfuniq - /usr/local/bin/vcfuniq [05:59:34] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:59:34] Found gzip - /bin/gzip [05:59:34] Found vt - /usr/local/bin/vt [05:59:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:59:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:59:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:59:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:59:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:59:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:59:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:59:35] Using reference: /cvmfs/data.galaxyproject.org/byhand/microbes/eschColi_APEC_O1/seq/eschColi_APEC_O1.fa [05:59:35] Treating reference as 'fasta' format. [05:59:35] Will use 1 CPU cores. [05:59:35] Using read file: /corral4/main/objects/d/b/3/dataset_db3cd7c8-47c4-4b64-baf8-c75df54fe65c.dat [05:59:35] Creating folder: Resistance_76_fasta [05:59:35] Changing working directory: Resistance_76_fasta [05:59:35] Creating reference folder: reference [05:59:35] Extracting FASTA and GFF from reference. [05:59:35] Wrote 3 sequences to ref.fa [05:59:35] Wrote 0 features to ref.gff [05:59:35] Shredding /corral4/main/objects/d/b/3/dataset_db3cd7c8-47c4-4b64-baf8-c75df54fe65c.dat into pseudo-reads [05:59:40] Wrote 432130 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [05:59:40] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time. [05:59:40] Using BAM RG (Read Group) ID: Resistance_76_fasta [05:59:40] Running: samtools faidx reference/ref.fa 2>> snps.log [05:59:40] Error running command, check Resistance_76_fasta/snps.log
2[05:59:14] This is snippy 4.6.0
Show full stderr[05:59:14] This is snippy 4.6.0 [05:59:14] Written by Torsten Seemann [05:59:14] Obtained from https://github.com/tseemann/snippy [05:59:14] Detected operating system: linux [05:59:14] Enabling bundled linux tools. [05:59:14] Found bwa - /usr/local/bin/bwa [05:59:14] Found bcftools - /usr/local/bin/bcftools [05:59:14] Found samtools - /usr/local/bin/samtools [05:59:14] Found java - /usr/local/bin/java [05:59:14] Found snpEff - /usr/local/bin/snpEff [05:59:14] Found samclip - /usr/local/bin/samclip [05:59:14] Found seqtk - /usr/local/bin/seqtk [05:59:14] Found parallel - /usr/local/bin/parallel [05:59:14] Found freebayes - /usr/local/bin/freebayes [05:59:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:59:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:59:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:59:14] Found vcfuniq - /usr/local/bin/vcfuniq [05:59:14] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:59:14] Found gzip - /bin/gzip [05:59:14] Found vt - /usr/local/bin/vt [05:59:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:59:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:59:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:59:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:59:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:59:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:59:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:59:16] Using reference: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat [05:59:16] Treating reference as 'fasta' format. [05:59:16] Will use 1 CPU cores. [05:59:16] Using read file: /corral4/main/objects/f/6/7/dataset_f670061e-7fa9-400e-85f8-fee756398e62.dat [05:59:16] Creating folder: GCF_001191715_1_5505_8_8_genomic_fna [05:59:16] Changing working directory: GCF_001191715_1_5505_8_8_genomic_fna [05:59:16] Creating reference folder: reference [05:59:16] Extracting FASTA and GFF from reference. [05:59:16] Wrote 1 sequences to ref.fa [05:59:16] Wrote 0 features to ref.gff [05:59:16] Shredding /corral4/main/objects/f/6/7/dataset_f670061e-7fa9-400e-85f8-fee756398e62.dat into pseudo-reads [05:59:20] Wrote 351090 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [05:59:21] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time. [05:59:21] Using BAM RG (Read Group) ID: GCF_001191715_1_5505_8_8_genomic_fna [05:59:21] Running: samtools faidx reference/ref.fa 2>> snps.log [05:59:22] Error running command, check GCF_001191715_1_5505_8_8_genomic_fna/snps.log
2[05:59:58] This is snippy 4.6.0
Show full stderr[05:59:58] This is snippy 4.6.0 [05:59:58] Written by Torsten Seemann [05:59:58] Obtained from https://github.com/tseemann/snippy [05:59:58] Detected operating system: linux [05:59:58] Enabling bundled linux tools. [05:59:58] Found bwa - /usr/local/bin/bwa [05:59:58] Found bcftools - /usr/local/bin/bcftools [05:59:58] Found samtools - /usr/local/bin/samtools [05:59:58] Found java - /usr/local/bin/java [05:59:58] Found snpEff - /usr/local/bin/snpEff [05:59:58] Found samclip - /usr/local/bin/samclip [05:59:58] Found seqtk - /usr/local/bin/seqtk [05:59:58] Found parallel - /usr/local/bin/parallel [05:59:58] Found freebayes - /usr/local/bin/freebayes [05:59:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:59:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:59:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:59:58] Found vcfuniq - /usr/local/bin/vcfuniq [05:59:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:59:58] Found gzip - /bin/gzip [05:59:58] Found vt - /usr/local/bin/vt [05:59:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:59:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:59:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:59:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:59:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:59:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:59:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:59:59] Using reference: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat [05:59:59] Treating reference as 'fasta' format. [05:59:59] Will use 1 CPU cores. [05:59:59] Using read file: /corral4/main/objects/a/a/a/dataset_aaa5152b-fa66-4f0a-afc0-240761d2e97c.dat [05:59:59] Creating folder: GCF_903992715_1_Q1142_genomic_fna [05:59:59] Changing working directory: GCF_903992715_1_Q1142_genomic_fna [05:59:59] Creating reference folder: reference [05:59:59] Extracting FASTA and GFF from reference. [06:00:00] Wrote 1 sequences to ref.fa [06:00:00] Wrote 0 features to ref.gff [06:00:00] Shredding /corral4/main/objects/a/a/a/dataset_aaa5152b-fa66-4f0a-afc0-240761d2e97c.dat into pseudo-reads [06:00:03] Wrote 352422 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [06:00:04] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time. [06:00:04] Using BAM RG (Read Group) ID: GCF_903992715_1_Q1142_genomic_fna [06:00:04] Running: samtools faidx reference/ref.fa 2>> snps.log [06:00:04] Error running command, check GCF_903992715_1_Q1142_genomic_fna/snps.log
2[06:00:07] This is snippy 4.6.0
Show full stderr[06:00:07] This is snippy 4.6.0 [06:00:07] Written by Torsten Seemann [06:00:07] Obtained from https://github.com/tseemann/snippy [06:00:07] Detected operating system: linux [06:00:07] Enabling bundled linux tools. [06:00:07] Found bwa - /usr/local/bin/bwa [06:00:07] Found bcftools - /usr/local/bin/bcftools [06:00:07] Found samtools - /usr/local/bin/samtools [06:00:07] Found java - /usr/local/bin/java [06:00:07] Found snpEff - /usr/local/bin/snpEff [06:00:07] Found samclip - /usr/local/bin/samclip [06:00:07] Found seqtk - /usr/local/bin/seqtk [06:00:07] Found parallel - /usr/local/bin/parallel [06:00:07] Found freebayes - /usr/local/bin/freebayes [06:00:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:00:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:00:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:00:07] Found vcfuniq - /usr/local/bin/vcfuniq [06:00:07] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:00:07] Found gzip - /bin/gzip [06:00:07] Found vt - /usr/local/bin/vt [06:00:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:00:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:00:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:00:08] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:00:08] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:00:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:00:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:00:08] Using reference: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat [06:00:08] Treating reference as 'fasta' format. [06:00:08] Will use 1 CPU cores. [06:00:08] Using read file: /corral4/main/objects/2/5/d/dataset_25d0c2c3-35fe-47ff-a0ea-cd467baf8001.dat [06:00:08] Creating folder: GCF_020536615_1_ASM2053661v1_genomic_fna [06:00:08] Changing working directory: GCF_020536615_1_ASM2053661v1_genomic_fna [06:00:08] Creating reference folder: reference [06:00:08] Extracting FASTA and GFF from reference. [06:00:08] Wrote 1 sequences to ref.fa [06:00:08] Wrote 0 features to ref.gff [06:00:08] Shredding /corral4/main/objects/2/5/d/dataset_25d0c2c3-35fe-47ff-a0ea-cd467baf8001.dat into pseudo-reads [06:00:12] Wrote 349012 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [06:00:12] Freebayes will process 1 chunks of 4485121 bp, 1 chunks at a time. [06:00:12] Using BAM RG (Read Group) ID: GCF_020536615_1_ASM2053661v1_genomic_fna [06:00:12] Running: samtools faidx reference/ref.fa 2>> snps.log [06:00:12] Running: bwa index reference/ref.fa 2>> snps.log [06:00:14] Error running command, check GCF_020536615_1_ASM2053661v1_genomic_fna/snps.log
2[06:00:20] This is snippy 4.6.0
Show full stderr[06:00:20] This is snippy 4.6.0 [06:00:20] Written by Torsten Seemann [06:00:20] Obtained from https://github.com/tseemann/snippy [06:00:20] Detected operating system: linux [06:00:20] Enabling bundled linux tools. [06:00:20] Found bwa - /usr/local/bin/bwa [06:00:20] Found bcftools - /usr/local/bin/bcftools [06:00:20] Found samtools - /usr/local/bin/samtools [06:00:20] Found java - /usr/local/bin/java [06:00:20] Found snpEff - /usr/local/bin/snpEff [06:00:20] Found samclip - /usr/local/bin/samclip [06:00:20] Found seqtk - /usr/local/bin/seqtk [06:00:20] Found parallel - /usr/local/bin/parallel [06:00:20] Found freebayes - /usr/local/bin/freebayes [06:00:20] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:00:20] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:00:20] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:00:20] Found vcfuniq - /usr/local/bin/vcfuniq [06:00:20] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:00:20] Found gzip - /bin/gzip [06:00:20] Found vt - /usr/local/bin/vt [06:00:20] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:00:20] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:00:20] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:00:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:00:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:00:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:00:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:00:21] Using reference: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat [06:00:21] Treating reference as 'fasta' format. [06:00:21] Will use 1 CPU cores. [06:00:21] Using read file: /corral4/main/objects/8/6/b/dataset_86be6f76-47ba-48f2-a1e3-44d60b33078a.dat [06:00:21] Creating folder: GCF_902509475_1_Q0209_genomic_fna [06:00:21] Changing working directory: GCF_902509475_1_Q0209_genomic_fna [06:00:21] Creating reference folder: reference [06:00:21] Extracting FASTA and GFF from reference. [06:00:21] Wrote 1 sequences to ref.fa [06:00:21] Wrote 0 features to ref.gff [06:00:21] Shredding /corral4/main/objects/8/6/b/dataset_86be6f76-47ba-48f2-a1e3-44d60b33078a.dat into pseudo-reads [06:00:24] Wrote 347750 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [06:00:24] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time. [06:00:24] Using BAM RG (Read Group) ID: GCF_902509475_1_Q0209_genomic_fna [06:00:24] Running: samtools faidx reference/ref.fa 2>> snps.log [06:00:24] Error running command, check GCF_902509475_1_Q0209_genomic_fna/snps.log
2[06:58:21] This is snippy 4.6.0
Show full stderr[06:58:21] This is snippy 4.6.0 [06:58:21] Written by Torsten Seemann [06:58:21] Obtained from https://github.com/tseemann/snippy [06:58:21] Detected operating system: linux [06:58:21] Enabling bundled linux tools. [06:58:21] Found bwa - /usr/local/bin/bwa [06:58:21] Found bcftools - /usr/local/bin/bcftools [06:58:21] Found samtools - /usr/local/bin/samtools [06:58:21] Found java - /usr/local/bin/java [06:58:21] Found snpEff - /usr/local/bin/snpEff [06:58:21] Found samclip - /usr/local/bin/samclip [06:58:21] Found seqtk - /usr/local/bin/seqtk [06:58:21] Found parallel - /usr/local/bin/parallel [06:58:21] Found freebayes - /usr/local/bin/freebayes [06:58:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:58:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:58:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:58:21] Found vcfuniq - /usr/local/bin/vcfuniq [06:58:21] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:58:21] Found gzip - /bin/gzip [06:58:21] Found vt - /usr/local/bin/vt [06:58:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:58:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:58:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:58:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:58:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:58:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:58:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:58:22] Using reference: /corral4/main/objects/b/c/7/dataset_bc72f994-0ee8-49f5-b32a-d0eb5858fef9.dat [06:58:22] Treating reference as 'fasta' format. [06:58:22] Will use 1 CPU cores. [06:58:22] Using read file: /corral4/main/objects/0/e/9/dataset_0e967aab-1d11-4057-ab74-1b27a9a4c8ef.dat [06:58:22] Creating folder: BVBRC_genome_sequence__78__fasta [06:58:22] Changing working directory: BVBRC_genome_sequence__78__fasta [06:58:22] Creating reference folder: reference [06:58:22] Extracting FASTA and GFF from reference. [06:58:22] Wrote 1 sequences to ref.fa [06:58:22] Wrote 0 features to ref.gff [06:58:22] Shredding /corral4/main/objects/0/e/9/dataset_0e967aab-1d11-4057-ab74-1b27a9a4c8ef.dat into pseudo-reads [06:58:24] Wrote 216932 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [06:58:24] Freebayes will process 1 chunks of 2868471 bp, 1 chunks at a time. [06:58:24] Using BAM RG (Read Group) ID: BVBRC_genome_sequence__78__fasta [06:58:24] Running: samtools faidx reference/ref.fa 2>> snps.log [06:58:24] Running: bwa index reference/ref.fa 2>> snps.log [06:58:26] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [06:58:26] Running: ln -sf reference/ref.fa . 2>> snps.log [06:58:26] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [06:58:26] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [06:58:26] Running: bwa mem -Y -M -R '@RG\tID:BVBRC_genome_sequence__78__fasta\tSM:BVBRC_genome_sequence__78__fasta' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/261/72261283/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/261/72261283/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/261/72261283/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [s
2[07:02:34] This is snippy 4.6.0
Show full stderr[07:02:34] This is snippy 4.6.0 [07:02:34] Written by Torsten Seemann [07:02:34] Obtained from https://github.com/tseemann/snippy [07:02:34] Detected operating system: linux [07:02:34] Enabling bundled linux tools. [07:02:34] Found bwa - /usr/local/bin/bwa [07:02:34] Found bcftools - /usr/local/bin/bcftools [07:02:34] Found samtools - /usr/local/bin/samtools [07:02:34] Found java - /usr/local/bin/java [07:02:34] Found snpEff - /usr/local/bin/snpEff [07:02:34] Found samclip - /usr/local/bin/samclip [07:02:34] Found seqtk - /usr/local/bin/seqtk [07:02:34] Found parallel - /usr/local/bin/parallel [07:02:34] Found freebayes - /usr/local/bin/freebayes [07:02:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:02:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:02:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:02:34] Found vcfuniq - /usr/local/bin/vcfuniq [07:02:34] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:02:34] Found gzip - /bin/gzip [07:02:34] Found vt - /usr/local/bin/vt [07:02:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:02:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:02:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:02:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:02:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:02:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:02:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:02:35] Using reference: /corral4/main/objects/b/c/7/dataset_bc72f994-0ee8-49f5-b32a-d0eb5858fef9.dat [07:02:35] Treating reference as 'fasta' format. [07:02:35] Will use 1 CPU cores. [07:02:35] Using read file: /corral4/main/objects/5/9/5/dataset_5955a17d-5755-4d34-b4d0-d5f37647b470.dat [07:02:35] Creating folder: BVBRC_genome_sequence___2025_10_25T135642_512_fasta [07:02:35] Changing working directory: BVBRC_genome_sequence___2025_10_25T135642_512_fasta [07:02:35] Creating reference folder: reference [07:02:35] Extracting FASTA and GFF from reference. [07:02:35] Wrote 1 sequences to ref.fa [07:02:35] Wrote 0 features to ref.gff [07:02:35] Shredding /corral4/main/objects/5/9/5/dataset_5955a17d-5755-4d34-b4d0-d5f37647b470.dat into pseudo-reads [07:02:37] Wrote 222668 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [07:02:37] Freebayes will process 1 chunks of 2868471 bp, 1 chunks at a time. [07:02:37] Using BAM RG (Read Group) ID: BVBRC_genome_sequence___2025_10_25T135642_512_fasta [07:02:37] Running: samtools faidx reference/ref.fa 2>> snps.log [07:02:37] Running: bwa index reference/ref.fa 2>> snps.log [07:02:38] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [07:02:38] Running: ln -sf reference/ref.fa . 2>> snps.log [07:02:38] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [07:02:38] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [07:02:38] Running: bwa mem -Y -M -R '@RG\tID:BVBRC_genome_sequence___2025_10_25T135642_512_fasta\tSM:BVBRC_genome_sequence___2025_10_25T135642_512_fasta' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/261/72261358/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/261/72261358/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/261/72261358/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samcl
2[07:05:38] This is snippy 4.6.0
Show full stderr[07:05:38] This is snippy 4.6.0 [07:05:38] Written by Torsten Seemann [07:05:38] Obtained from https://github.com/tseemann/snippy [07:05:38] Detected operating system: linux [07:05:38] Enabling bundled linux tools. [07:05:38] Found bwa - /usr/local/bin/bwa [07:05:38] Found bcftools - /usr/local/bin/bcftools [07:05:38] Found samtools - /usr/local/bin/samtools [07:05:38] Found java - /usr/local/bin/java [07:05:38] Found snpEff - /usr/local/bin/snpEff [07:05:38] Found samclip - /usr/local/bin/samclip [07:05:38] Found seqtk - /usr/local/bin/seqtk [07:05:38] Found parallel - /usr/local/bin/parallel [07:05:38] Found freebayes - /usr/local/bin/freebayes [07:05:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:05:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:05:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:05:38] Found vcfuniq - /usr/local/bin/vcfuniq [07:05:38] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:05:38] Found gzip - /bin/gzip [07:05:38] Found vt - /usr/local/bin/vt [07:05:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:05:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:05:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:05:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:05:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:05:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:05:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:05:39] Using reference: /corral4/main/objects/b/c/7/dataset_bc72f994-0ee8-49f5-b32a-d0eb5858fef9.dat [07:05:39] Treating reference as 'fasta' format. [07:05:39] Will use 1 CPU cores. [07:05:39] Using read file: /corral4/main/objects/3/2/7/dataset_3270deb9-a273-4d32-9777-15dcab5bd02b.dat [07:05:39] Creating folder: BVBRC_genome_sequence___2025_10_25T135710_500_fasta [07:05:39] Changing working directory: BVBRC_genome_sequence___2025_10_25T135710_500_fasta [07:05:39] Creating reference folder: reference [07:05:39] Extracting FASTA and GFF from reference. [07:05:39] Wrote 1 sequences to ref.fa [07:05:39] Wrote 0 features to ref.gff [07:05:39] Shredding /corral4/main/objects/3/2/7/dataset_3270deb9-a273-4d32-9777-15dcab5bd02b.dat into pseudo-reads [07:05:41] Wrote 222136 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [07:05:41] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time. [07:05:41] Using BAM RG (Read Group) ID: BVBRC_genome_sequence___2025_10_25T135710_500_fasta [07:05:41] Running: samtools faidx reference/ref.fa 2>> snps.log [07:05:41] Error running command, check BVBRC_genome_sequence___2025_10_25T135710_500_fasta/snps.log
2[07:05:54] This is snippy 4.6.0
Show full stderr[07:05:54] This is snippy 4.6.0 [07:05:54] Written by Torsten Seemann [07:05:54] Obtained from https://github.com/tseemann/snippy [07:05:54] Detected operating system: linux [07:05:54] Enabling bundled linux tools. [07:05:54] Found bwa - /usr/local/bin/bwa [07:05:54] Found bcftools - /usr/local/bin/bcftools [07:05:54] Found samtools - /usr/local/bin/samtools [07:05:54] Found java - /usr/local/bin/java [07:05:54] Found snpEff - /usr/local/bin/snpEff [07:05:54] Found samclip - /usr/local/bin/samclip [07:05:54] Found seqtk - /usr/local/bin/seqtk [07:05:54] Found parallel - /usr/local/bin/parallel [07:05:54] Found freebayes - /usr/local/bin/freebayes [07:05:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:05:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:05:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:05:54] Found vcfuniq - /usr/local/bin/vcfuniq [07:05:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:05:54] Found gzip - /bin/gzip [07:05:54] Found vt - /usr/local/bin/vt [07:05:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:05:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:05:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:05:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:05:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:05:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:05:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:05:55] Using reference: /corral4/main/objects/b/c/7/dataset_bc72f994-0ee8-49f5-b32a-d0eb5858fef9.dat [07:05:55] Treating reference as 'fasta' format. [07:05:55] Will use 1 CPU cores. [07:05:55] Using read file: /corral4/main/objects/5/a/2/dataset_5a2a9927-9c17-4e2c-9090-63a02a9141b0.dat [07:05:55] Creating folder: BVBRC_genome_sequence___2025_10_25T135715_719_fasta [07:05:55] Changing working directory: BVBRC_genome_sequence___2025_10_25T135715_719_fasta [07:05:55] Creating reference folder: reference [07:05:55] Extracting FASTA and GFF from reference. [07:05:55] Wrote 1 sequences to ref.fa [07:05:55] Wrote 0 features to ref.gff [07:05:55] Shredding /corral4/main/objects/5/a/2/dataset_5a2a9927-9c17-4e2c-9090-63a02a9141b0.dat into pseudo-reads [07:05:57] Wrote 224908 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [07:05:57] Freebayes will process 1 chunks of 2868471 bp, 1 chunks at a time. [07:05:57] Using BAM RG (Read Group) ID: BVBRC_genome_sequence___2025_10_25T135715_719_fasta [07:05:57] Running: samtools faidx reference/ref.fa 2>> snps.log [07:05:57] Running: bwa index reference/ref.fa 2>> snps.log [07:05:59] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [07:05:59] Running: ln -sf reference/ref.fa . 2>> snps.log [07:05:59] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [07:05:59] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [07:05:59] Running: bwa mem -Y -M -R '@RG\tID:BVBRC_genome_sequence___2025_10_25T135715_719_fasta\tSM:BVBRC_genome_sequence___2025_10_25T135715_719_fasta' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/261/72261365/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/261/72261365/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/261/72261365/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
2[06:47:56] This is snippy 4.6.0
Show full stderr[06:47:56] This is snippy 4.6.0 [06:47:56] Written by Torsten Seemann [06:47:56] Obtained from https://github.com/tseemann/snippy [06:47:56] Detected operating system: linux [06:47:56] Enabling bundled linux tools. [06:47:56] Found bwa - /usr/local/bin/bwa [06:47:56] Found bcftools - /usr/local/bin/bcftools [06:47:56] Found samtools - /usr/local/bin/samtools [06:47:56] Found java - /usr/local/bin/java [06:47:56] Found snpEff - /usr/local/bin/snpEff [06:47:56] Found samclip - /usr/local/bin/samclip [06:47:56] Found seqtk - /usr/local/bin/seqtk [06:47:56] Found parallel - /usr/local/bin/parallel [06:47:56] Found freebayes - /usr/local/bin/freebayes [06:47:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:47:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:47:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:47:56] Found vcfuniq - /usr/local/bin/vcfuniq [06:47:56] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:47:56] Found gzip - /bin/gzip [06:47:56] Found vt - /usr/local/bin/vt [06:47:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:47:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:47:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:47:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:47:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:47:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:47:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:47:56] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:00:09] This is snippy 4.6.0
Show full stderr[07:00:09] This is snippy 4.6.0 [07:00:09] Written by Torsten Seemann [07:00:09] Obtained from https://github.com/tseemann/snippy [07:00:09] Detected operating system: linux [07:00:09] Enabling bundled linux tools. [07:00:09] Found bwa - /usr/local/bin/bwa [07:00:09] Found bcftools - /usr/local/bin/bcftools [07:00:09] Found samtools - /usr/local/bin/samtools [07:00:09] Found java - /usr/local/bin/java [07:00:09] Found snpEff - /usr/local/bin/snpEff [07:00:09] Found samclip - /usr/local/bin/samclip [07:00:09] Found seqtk - /usr/local/bin/seqtk [07:00:09] Found parallel - /usr/local/bin/parallel [07:00:09] Found freebayes - /usr/local/bin/freebayes [07:00:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:00:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:00:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:00:09] Found vcfuniq - /usr/local/bin/vcfuniq [07:00:09] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:00:09] Found gzip - /bin/gzip [07:00:09] Found vt - /usr/local/bin/vt [07:00:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:00:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:00:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:00:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:00:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:00:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:00:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:00:10] Please supply a reference FASTA/GBK/EMBL file with --reference
2[06:49:07] This is snippy 4.6.0
Show full stderr[06:49:07] This is snippy 4.6.0 [06:49:07] Written by Torsten Seemann [06:49:07] Obtained from https://github.com/tseemann/snippy [06:49:07] Detected operating system: linux [06:49:07] Enabling bundled linux tools. [06:49:07] Found bwa - /usr/local/bin/bwa [06:49:07] Found bcftools - /usr/local/bin/bcftools [06:49:07] Found samtools - /usr/local/bin/samtools [06:49:07] Found java - /usr/local/bin/java [06:49:07] Found snpEff - /usr/local/bin/snpEff [06:49:07] Found samclip - /usr/local/bin/samclip [06:49:07] Found seqtk - /usr/local/bin/seqtk [06:49:07] Found parallel - /usr/local/bin/parallel [06:49:07] Found freebayes - /usr/local/bin/freebayes [06:49:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:49:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:49:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:49:07] Found vcfuniq - /usr/local/bin/vcfuniq [06:49:07] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:49:07] Found gzip - /bin/gzip [06:49:07] Found vt - /usr/local/bin/vt [06:49:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:49:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:49:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:49:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:49:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:49:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:49:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:49:08] Please supply a reference FASTA/GBK/EMBL file with --reference
2[06:49:10] This is snippy 4.6.0
Show full stderr[06:49:10] This is snippy 4.6.0 [06:49:10] Written by Torsten Seemann [06:49:10] Obtained from https://github.com/tseemann/snippy [06:49:10] Detected operating system: linux [06:49:10] Enabling bundled linux tools. [06:49:10] Found bwa - /usr/local/bin/bwa [06:49:10] Found bcftools - /usr/local/bin/bcftools [06:49:10] Found samtools - /usr/local/bin/samtools [06:49:10] Found java - /usr/local/bin/java [06:49:10] Found snpEff - /usr/local/bin/snpEff [06:49:10] Found samclip - /usr/local/bin/samclip [06:49:10] Found seqtk - /usr/local/bin/seqtk [06:49:10] Found parallel - /usr/local/bin/parallel [06:49:10] Found freebayes - /usr/local/bin/freebayes [06:49:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:49:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:49:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:49:10] Found vcfuniq - /usr/local/bin/vcfuniq [06:49:10] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:49:10] Found gzip - /bin/gzip [06:49:10] Found vt - /usr/local/bin/vt [06:49:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:49:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:49:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:49:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:49:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:49:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:49:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:49:11] Please supply a reference FASTA/GBK/EMBL file with --reference
2[06:49:22] This is snippy 4.6.0
Show full stderr[06:49:22] This is snippy 4.6.0 [06:49:22] Written by Torsten Seemann [06:49:22] Obtained from https://github.com/tseemann/snippy [06:49:22] Detected operating system: linux [06:49:22] Enabling bundled linux tools. [06:49:22] Found bwa - /usr/local/bin/bwa [06:49:22] Found bcftools - /usr/local/bin/bcftools [06:49:22] Found samtools - /usr/local/bin/samtools [06:49:22] Found java - /usr/local/bin/java [06:49:22] Found snpEff - /usr/local/bin/snpEff [06:49:22] Found samclip - /usr/local/bin/samclip [06:49:22] Found seqtk - /usr/local/bin/seqtk [06:49:22] Found parallel - /usr/local/bin/parallel [06:49:22] Found freebayes - /usr/local/bin/freebayes [06:49:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:49:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:49:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:49:22] Found vcfuniq - /usr/local/bin/vcfuniq [06:49:22] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:49:22] Found gzip - /bin/gzip [06:49:22] Found vt - /usr/local/bin/vt [06:49:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:49:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:49:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:49:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:49:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:49:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:49:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:49:23] Please supply a reference FASTA/GBK/EMBL file with --reference
2[06:53:48] This is snippy 4.6.0
Show full stderr[06:53:48] This is snippy 4.6.0 [06:53:48] Written by Torsten Seemann [06:53:48] Obtained from https://github.com/tseemann/snippy [06:53:48] Detected operating system: linux [06:53:48] Enabling bundled linux tools. [06:53:48] Found bwa - /usr/local/bin/bwa [06:53:48] Found bcftools - /usr/local/bin/bcftools [06:53:48] Found samtools - /usr/local/bin/samtools [06:53:48] Found java - /usr/local/bin/java [06:53:48] Found snpEff - /usr/local/bin/snpEff [06:53:48] Found samclip - /usr/local/bin/samclip [06:53:48] Found seqtk - /usr/local/bin/seqtk [06:53:48] Found parallel - /usr/local/bin/parallel [06:53:48] Found freebayes - /usr/local/bin/freebayes [06:53:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:53:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:53:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:53:48] Found vcfuniq - /usr/local/bin/vcfuniq [06:53:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:53:48] Found gzip - /bin/gzip [06:53:48] Found vt - /usr/local/bin/vt [06:53:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:53:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:53:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:53:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:53:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:53:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:53:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:53:49] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:00:10] This is snippy 4.6.0
Show full stderr[07:00:10] This is snippy 4.6.0 [07:00:10] Written by Torsten Seemann [07:00:10] Obtained from https://github.com/tseemann/snippy [07:00:10] Detected operating system: linux [07:00:10] Enabling bundled linux tools. [07:00:10] Found bwa - /usr/local/bin/bwa [07:00:10] Found bcftools - /usr/local/bin/bcftools [07:00:10] Found samtools - /usr/local/bin/samtools [07:00:10] Found java - /usr/local/bin/java [07:00:10] Found snpEff - /usr/local/bin/snpEff [07:00:10] Found samclip - /usr/local/bin/samclip [07:00:10] Found seqtk - /usr/local/bin/seqtk [07:00:10] Found parallel - /usr/local/bin/parallel [07:00:10] Found freebayes - /usr/local/bin/freebayes [07:00:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:00:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:00:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:00:10] Found vcfuniq - /usr/local/bin/vcfuniq [07:00:10] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:00:10] Found gzip - /bin/gzip [07:00:10] Found vt - /usr/local/bin/vt [07:00:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:00:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:00:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:00:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:00:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:00:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:00:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:00:10] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:07:28] This is snippy 4.6.0
Show full stderr[07:07:28] This is snippy 4.6.0 [07:07:28] Written by Torsten Seemann [07:07:28] Obtained from https://github.com/tseemann/snippy [07:07:28] Detected operating system: linux [07:07:28] Enabling bundled linux tools. [07:07:28] Found bwa - /usr/local/bin/bwa [07:07:28] Found bcftools - /usr/local/bin/bcftools [07:07:28] Found samtools - /usr/local/bin/samtools [07:07:28] Found java - /usr/local/bin/java [07:07:28] Found snpEff - /usr/local/bin/snpEff [07:07:28] Found samclip - /usr/local/bin/samclip [07:07:28] Found seqtk - /usr/local/bin/seqtk [07:07:28] Found parallel - /usr/local/bin/parallel [07:07:28] Found freebayes - /usr/local/bin/freebayes [07:07:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:07:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:07:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:07:28] Found vcfuniq - /usr/local/bin/vcfuniq [07:07:28] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:07:28] Found gzip - /bin/gzip [07:07:28] Found vt - /usr/local/bin/vt [07:07:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:07:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:07:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:07:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:07:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:07:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:07:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:07:29] Please supply a reference FASTA/GBK/EMBL file with --reference
2[06:48:39] This is snippy 4.6.0
Show full stderr[06:48:39] This is snippy 4.6.0 [06:48:39] Written by Torsten Seemann [06:48:39] Obtained from https://github.com/tseemann/snippy [06:48:39] Detected operating system: linux [06:48:39] Enabling bundled linux tools. [06:48:39] Found bwa - /usr/local/bin/bwa [06:48:39] Found bcftools - /usr/local/bin/bcftools [06:48:39] Found samtools - /usr/local/bin/samtools [06:48:39] Found java - /usr/local/bin/java [06:48:39] Found snpEff - /usr/local/bin/snpEff [06:48:39] Found samclip - /usr/local/bin/samclip [06:48:39] Found seqtk - /usr/local/bin/seqtk [06:48:39] Found parallel - /usr/local/bin/parallel [06:48:39] Found freebayes - /usr/local/bin/freebayes [06:48:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:48:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:48:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:48:39] Found vcfuniq - /usr/local/bin/vcfuniq [06:48:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:48:39] Found gzip - /bin/gzip [06:48:39] Found vt - /usr/local/bin/vt [06:48:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:48:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:48:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:48:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:48:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:48:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:48:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:48:40] Please supply a reference FASTA/GBK/EMBL file with --reference
2[06:49:36] This is snippy 4.6.0
Show full stderr[06:49:36] This is snippy 4.6.0 [06:49:36] Written by Torsten Seemann [06:49:36] Obtained from https://github.com/tseemann/snippy [06:49:36] Detected operating system: linux [06:49:36] Enabling bundled linux tools. [06:49:36] Found bwa - /usr/local/bin/bwa [06:49:36] Found bcftools - /usr/local/bin/bcftools [06:49:36] Found samtools - /usr/local/bin/samtools [06:49:36] Found java - /usr/local/bin/java [06:49:36] Found snpEff - /usr/local/bin/snpEff [06:49:36] Found samclip - /usr/local/bin/samclip [06:49:36] Found seqtk - /usr/local/bin/seqtk [06:49:36] Found parallel - /usr/local/bin/parallel [06:49:36] Found freebayes - /usr/local/bin/freebayes [06:49:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:49:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:49:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:49:36] Found vcfuniq - /usr/local/bin/vcfuniq [06:49:36] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:49:36] Found gzip - /bin/gzip [06:49:36] Found vt - /usr/local/bin/vt [06:49:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:49:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:49:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:49:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:49:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:49:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:49:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:49:37] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:38:54] This is snippy 4.6.0
Show full stderr[07:38:54] This is snippy 4.6.0 [07:38:54] Written by Torsten Seemann [07:38:54] Obtained from https://github.com/tseemann/snippy [07:38:54] Detected operating system: linux [07:38:54] Enabling bundled linux tools. [07:38:54] Found bwa - /usr/local/bin/bwa [07:38:54] Found bcftools - /usr/local/bin/bcftools [07:38:54] Found samtools - /usr/local/bin/samtools [07:38:54] Found java - /usr/local/bin/java [07:38:54] Found snpEff - /usr/local/bin/snpEff [07:38:54] Found samclip - /usr/local/bin/samclip [07:38:54] Found seqtk - /usr/local/bin/seqtk [07:38:54] Found parallel - /usr/local/bin/parallel [07:38:54] Found freebayes - /usr/local/bin/freebayes [07:38:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:38:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:38:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:38:54] Found vcfuniq - /usr/local/bin/vcfuniq [07:38:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:38:54] Found gzip - /bin/gzip [07:38:54] Found vt - /usr/local/bin/vt [07:38:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:38:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:38:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:38:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:38:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:38:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:38:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:38:55] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:45:13] This is snippy 4.6.0
Show full stderr[07:45:13] This is snippy 4.6.0 [07:45:13] Written by Torsten Seemann [07:45:13] Obtained from https://github.com/tseemann/snippy [07:45:13] Detected operating system: linux [07:45:13] Enabling bundled linux tools. [07:45:13] Found bwa - /usr/local/bin/bwa [07:45:13] Found bcftools - /usr/local/bin/bcftools [07:45:13] Found samtools - /usr/local/bin/samtools [07:45:13] Found java - /usr/local/bin/java [07:45:13] Found snpEff - /usr/local/bin/snpEff [07:45:13] Found samclip - /usr/local/bin/samclip [07:45:13] Found seqtk - /usr/local/bin/seqtk [07:45:13] Found parallel - /usr/local/bin/parallel [07:45:13] Found freebayes - /usr/local/bin/freebayes [07:45:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:45:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:45:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:45:13] Found vcfuniq - /usr/local/bin/vcfuniq [07:45:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:45:13] Found gzip - /bin/gzip [07:45:13] Found vt - /usr/local/bin/vt [07:45:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:45:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:45:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:45:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:45:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:45:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:45:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:45:14] Please supply a reference FASTA/GBK/EMBL file with --reference
2[06:51:04] This is snippy 4.6.0
Show full stderr[06:51:04] This is snippy 4.6.0 [06:51:04] Written by Torsten Seemann [06:51:04] Obtained from https://github.com/tseemann/snippy [06:51:04] Detected operating system: linux [06:51:04] Enabling bundled linux tools. [06:51:04] Found bwa - /usr/local/bin/bwa [06:51:04] Found bcftools - /usr/local/bin/bcftools [06:51:04] Found samtools - /usr/local/bin/samtools [06:51:04] Found java - /usr/local/bin/java [06:51:04] Found snpEff - /usr/local/bin/snpEff [06:51:04] Found samclip - /usr/local/bin/samclip [06:51:04] Found seqtk - /usr/local/bin/seqtk [06:51:04] Found parallel - /usr/local/bin/parallel [06:51:04] Found freebayes - /usr/local/bin/freebayes [06:51:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:51:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:51:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:51:04] Found vcfuniq - /usr/local/bin/vcfuniq [06:51:04] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:51:04] Found gzip - /bin/gzip [06:51:04] Found vt - /usr/local/bin/vt [06:51:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:51:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:51:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:51:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:51:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:51:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:51:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:51:05] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:51:15] This is snippy 4.6.0
Show full stderr[07:51:15] This is snippy 4.6.0 [07:51:15] Written by Torsten Seemann [07:51:15] Obtained from https://github.com/tseemann/snippy [07:51:15] Detected operating system: linux [07:51:15] Enabling bundled linux tools. [07:51:15] Found bwa - /usr/local/bin/bwa [07:51:15] Found bcftools - /usr/local/bin/bcftools [07:51:15] Found samtools - /usr/local/bin/samtools [07:51:15] Found java - /usr/local/bin/java [07:51:15] Found snpEff - /usr/local/bin/snpEff [07:51:15] Found samclip - /usr/local/bin/samclip [07:51:15] Found seqtk - /usr/local/bin/seqtk [07:51:15] Found parallel - /usr/local/bin/parallel [07:51:15] Found freebayes - /usr/local/bin/freebayes [07:51:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:51:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:51:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:51:15] Found vcfuniq - /usr/local/bin/vcfuniq [07:51:15] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:51:15] Found gzip - /bin/gzip [07:51:15] Found vt - /usr/local/bin/vt [07:51:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:51:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:51:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:51:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:51:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:51:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:51:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:51:16] Please supply a reference FASTA/GBK/EMBL file with --reference
2[06:51:14] This is snippy 4.6.0
Show full stderr[06:51:14] This is snippy 4.6.0 [06:51:14] Written by Torsten Seemann [06:51:14] Obtained from https://github.com/tseemann/snippy [06:51:14] Detected operating system: linux [06:51:14] Enabling bundled linux tools. [06:51:14] Found bwa - /usr/local/bin/bwa [06:51:14] Found bcftools - /usr/local/bin/bcftools [06:51:14] Found samtools - /usr/local/bin/samtools [06:51:14] Found java - /usr/local/bin/java [06:51:14] Found snpEff - /usr/local/bin/snpEff [06:51:14] Found samclip - /usr/local/bin/samclip [06:51:14] Found seqtk - /usr/local/bin/seqtk [06:51:14] Found parallel - /usr/local/bin/parallel [06:51:14] Found freebayes - /usr/local/bin/freebayes [06:51:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:51:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:51:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:51:14] Found vcfuniq - /usr/local/bin/vcfuniq [06:51:14] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:51:14] Found gzip - /bin/gzip [06:51:14] Found vt - /usr/local/bin/vt [06:51:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:51:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:51:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:51:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:51:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:51:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:51:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:51:15] Please supply a reference FASTA/GBK/EMBL file with --reference
2[06:52:36] This is snippy 4.6.0
Show full stderr[06:52:36] This is snippy 4.6.0 [06:52:36] Written by Torsten Seemann [06:52:36] Obtained from https://github.com/tseemann/snippy [06:52:36] Detected operating system: linux [06:52:36] Enabling bundled linux tools. [06:52:36] Found bwa - /usr/local/bin/bwa [06:52:36] Found bcftools - /usr/local/bin/bcftools [06:52:36] Found samtools - /usr/local/bin/samtools [06:52:36] Found java - /usr/local/bin/java [06:52:36] Found snpEff - /usr/local/bin/snpEff [06:52:36] Found samclip - /usr/local/bin/samclip [06:52:36] Found seqtk - /usr/local/bin/seqtk [06:52:36] Found parallel - /usr/local/bin/parallel [06:52:36] Found freebayes - /usr/local/bin/freebayes [06:52:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:52:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:52:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:52:36] Found vcfuniq - /usr/local/bin/vcfuniq [06:52:36] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:52:36] Found gzip - /bin/gzip [06:52:36] Found vt - /usr/local/bin/vt [06:52:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:52:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:52:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:52:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:52:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:52:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:52:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:52:37] Please supply a reference FASTA/GBK/EMBL file with --reference
2[06:53:18] This is snippy 4.6.0
Show full stderr[06:53:18] This is snippy 4.6.0 [06:53:18] Written by Torsten Seemann [06:53:18] Obtained from https://github.com/tseemann/snippy [06:53:18] Detected operating system: linux [06:53:18] Enabling bundled linux tools. [06:53:18] Found bwa - /usr/local/bin/bwa [06:53:18] Found bcftools - /usr/local/bin/bcftools [06:53:18] Found samtools - /usr/local/bin/samtools [06:53:18] Found java - /usr/local/bin/java [06:53:18] Found snpEff - /usr/local/bin/snpEff [06:53:18] Found samclip - /usr/local/bin/samclip [06:53:18] Found seqtk - /usr/local/bin/seqtk [06:53:18] Found parallel - /usr/local/bin/parallel [06:53:18] Found freebayes - /usr/local/bin/freebayes [06:53:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:53:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:53:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:53:18] Found vcfuniq - /usr/local/bin/vcfuniq [06:53:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:53:18] Found gzip - /bin/gzip [06:53:18] Found vt - /usr/local/bin/vt [06:53:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:53:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:53:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:53:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:53:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:53:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:53:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:53:19] Please supply a reference FASTA/GBK/EMBL file with --reference
2[06:53:30] This is snippy 4.6.0
Show full stderr[06:53:30] This is snippy 4.6.0 [06:53:30] Written by Torsten Seemann [06:53:30] Obtained from https://github.com/tseemann/snippy [06:53:30] Detected operating system: linux [06:53:30] Enabling bundled linux tools. [06:53:30] Found bwa - /usr/local/bin/bwa [06:53:30] Found bcftools - /usr/local/bin/bcftools [06:53:30] Found samtools - /usr/local/bin/samtools [06:53:30] Found java - /usr/local/bin/java [06:53:30] Found snpEff - /usr/local/bin/snpEff [06:53:30] Found samclip - /usr/local/bin/samclip [06:53:30] Found seqtk - /usr/local/bin/seqtk [06:53:30] Found parallel - /usr/local/bin/parallel [06:53:30] Found freebayes - /usr/local/bin/freebayes [06:53:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:53:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:53:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:53:30] Found vcfuniq - /usr/local/bin/vcfuniq [06:53:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:53:30] Found gzip - /bin/gzip [06:53:30] Found vt - /usr/local/bin/vt [06:53:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:53:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:53:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:53:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:53:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:53:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:53:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:53:31] Please supply a reference FASTA/GBK/EMBL file with --reference
2[06:50:53] This is snippy 4.6.0
Show full stderr[06:50:53] This is snippy 4.6.0 [06:50:53] Written by Torsten Seemann [06:50:53] Obtained from https://github.com/tseemann/snippy [06:50:53] Detected operating system: linux [06:50:53] Enabling bundled linux tools. [06:50:53] Found bwa - /usr/local/bin/bwa [06:50:53] Found bcftools - /usr/local/bin/bcftools [06:50:53] Found samtools - /usr/local/bin/samtools [06:50:53] Found java - /usr/local/bin/java [06:50:53] Found snpEff - /usr/local/bin/snpEff [06:50:53] Found samclip - /usr/local/bin/samclip [06:50:53] Found seqtk - /usr/local/bin/seqtk [06:50:53] Found parallel - /usr/local/bin/parallel [06:50:53] Found freebayes - /usr/local/bin/freebayes [06:50:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:50:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:50:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:50:53] Found vcfuniq - /usr/local/bin/vcfuniq [06:50:53] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:50:53] Found gzip - /bin/gzip [06:50:53] Found vt - /usr/local/bin/vt [06:50:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:50:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:50:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:50:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:50:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:50:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:50:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:50:54] Please supply a reference FASTA/GBK/EMBL file with --reference
2[08:03:31] This is snippy 4.6.0
Show full stderr[08:03:31] This is snippy 4.6.0 [08:03:31] Written by Torsten Seemann [08:03:31] Obtained from https://github.com/tseemann/snippy [08:03:31] Detected operating system: linux [08:03:31] Enabling bundled linux tools. [08:03:31] Found bwa - /usr/local/bin/bwa [08:03:31] Found bcftools - /usr/local/bin/bcftools [08:03:31] Found samtools - /usr/local/bin/samtools [08:03:31] Found java - /usr/local/bin/java [08:03:31] Found snpEff - /usr/local/bin/snpEff [08:03:31] Found samclip - /usr/local/bin/samclip [08:03:31] Found seqtk - /usr/local/bin/seqtk [08:03:31] Found parallel - /usr/local/bin/parallel [08:03:31] Found freebayes - /usr/local/bin/freebayes [08:03:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:03:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:03:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:03:31] Found vcfuniq - /usr/local/bin/vcfuniq [08:03:31] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:03:31] Found gzip - /bin/gzip [08:03:31] Found vt - /usr/local/bin/vt [08:03:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:03:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:03:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:03:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:03:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:03:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:03:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:03:32] Please supply a reference FASTA/GBK/EMBL file with --reference
2[06:53:36] This is snippy 4.6.0
Show full stderr[06:53:36] This is snippy 4.6.0 [06:53:36] Written by Torsten Seemann [06:53:36] Obtained from https://github.com/tseemann/snippy [06:53:36] Detected operating system: linux [06:53:36] Enabling bundled linux tools. [06:53:36] Found bwa - /usr/local/bin/bwa [06:53:36] Found bcftools - /usr/local/bin/bcftools [06:53:36] Found samtools - /usr/local/bin/samtools [06:53:36] Found java - /usr/local/bin/java [06:53:36] Found snpEff - /usr/local/bin/snpEff [06:53:36] Found samclip - /usr/local/bin/samclip [06:53:36] Found seqtk - /usr/local/bin/seqtk [06:53:36] Found parallel - /usr/local/bin/parallel [06:53:36] Found freebayes - /usr/local/bin/freebayes [06:53:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:53:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:53:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:53:36] Found vcfuniq - /usr/local/bin/vcfuniq [06:53:36] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:53:36] Found gzip - /bin/gzip [06:53:36] Found vt - /usr/local/bin/vt [06:53:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:53:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:53:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:53:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:53:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:53:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:53:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:53:37] Please supply a reference FASTA/GBK/EMBL file with --reference
2[06:53:44] This is snippy 4.6.0
Show full stderr[06:53:44] This is snippy 4.6.0 [06:53:44] Written by Torsten Seemann [06:53:44] Obtained from https://github.com/tseemann/snippy [06:53:44] Detected operating system: linux [06:53:44] Enabling bundled linux tools. [06:53:44] Found bwa - /usr/local/bin/bwa [06:53:44] Found bcftools - /usr/local/bin/bcftools [06:53:44] Found samtools - /usr/local/bin/samtools [06:53:44] Found java - /usr/local/bin/java [06:53:44] Found snpEff - /usr/local/bin/snpEff [06:53:44] Found samclip - /usr/local/bin/samclip [06:53:44] Found seqtk - /usr/local/bin/seqtk [06:53:44] Found parallel - /usr/local/bin/parallel [06:53:44] Found freebayes - /usr/local/bin/freebayes [06:53:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:53:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:53:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:53:44] Found vcfuniq - /usr/local/bin/vcfuniq [06:53:44] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:53:44] Found gzip - /bin/gzip [06:53:44] Found vt - /usr/local/bin/vt [06:53:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:53:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:53:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:53:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:53:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:53:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:53:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:53:45] Please supply a reference FASTA/GBK/EMBL file with --reference
2[06:54:14] This is snippy 4.6.0
Show full stderr[06:54:14] This is snippy 4.6.0 [06:54:14] Written by Torsten Seemann [06:54:14] Obtained from https://github.com/tseemann/snippy [06:54:14] Detected operating system: linux [06:54:14] Enabling bundled linux tools. [06:54:14] Found bwa - /usr/local/bin/bwa [06:54:14] Found bcftools - /usr/local/bin/bcftools [06:54:14] Found samtools - /usr/local/bin/samtools [06:54:14] Found java - /usr/local/bin/java [06:54:14] Found snpEff - /usr/local/bin/snpEff [06:54:14] Found samclip - /usr/local/bin/samclip [06:54:14] Found seqtk - /usr/local/bin/seqtk [06:54:14] Found parallel - /usr/local/bin/parallel [06:54:14] Found freebayes - /usr/local/bin/freebayes [06:54:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:54:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:54:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:54:14] Found vcfuniq - /usr/local/bin/vcfuniq [06:54:14] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:54:14] Found gzip - /bin/gzip [06:54:14] Found vt - /usr/local/bin/vt [06:54:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:54:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:54:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:54:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:54:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:54:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:54:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:54:15] Please supply a reference FASTA/GBK/EMBL file with --reference
2[06:52:22] This is snippy 4.6.0
Show full stderr[06:52:22] This is snippy 4.6.0 [06:52:22] Written by Torsten Seemann [06:52:22] Obtained from https://github.com/tseemann/snippy [06:52:22] Detected operating system: linux [06:52:22] Enabling bundled linux tools. [06:52:22] Found bwa - /usr/local/bin/bwa [06:52:22] Found bcftools - /usr/local/bin/bcftools [06:52:22] Found samtools - /usr/local/bin/samtools [06:52:22] Found java - /usr/local/bin/java [06:52:22] Found snpEff - /usr/local/bin/snpEff [06:52:22] Found samclip - /usr/local/bin/samclip [06:52:22] Found seqtk - /usr/local/bin/seqtk [06:52:22] Found parallel - /usr/local/bin/parallel [06:52:22] Found freebayes - /usr/local/bin/freebayes [06:52:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:52:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:52:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:52:22] Found vcfuniq - /usr/local/bin/vcfuniq [06:52:22] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:52:22] Found gzip - /bin/gzip [06:52:22] Found vt - /usr/local/bin/vt [06:52:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:52:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:52:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:52:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:52:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:52:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:52:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:52:23] Please supply a reference FASTA/GBK/EMBL file with --reference
2[06:52:51] This is snippy 4.6.0
Show full stderr[06:52:51] This is snippy 4.6.0 [06:52:51] Written by Torsten Seemann [06:52:51] Obtained from https://github.com/tseemann/snippy [06:52:51] Detected operating system: linux [06:52:51] Enabling bundled linux tools. [06:52:51] Found bwa - /usr/local/bin/bwa [06:52:51] Found bcftools - /usr/local/bin/bcftools [06:52:51] Found samtools - /usr/local/bin/samtools [06:52:51] Found java - /usr/local/bin/java [06:52:51] Found snpEff - /usr/local/bin/snpEff [06:52:51] Found samclip - /usr/local/bin/samclip [06:52:51] Found seqtk - /usr/local/bin/seqtk [06:52:51] Found parallel - /usr/local/bin/parallel [06:52:51] Found freebayes - /usr/local/bin/freebayes [06:52:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:52:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:52:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:52:51] Found vcfuniq - /usr/local/bin/vcfuniq [06:52:51] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:52:51] Found gzip - /bin/gzip [06:52:51] Found vt - /usr/local/bin/vt [06:52:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:52:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:52:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:52:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:52:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:52:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:52:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:52:52] Please supply a reference FASTA/GBK/EMBL file with --reference
2[06:53:57] This is snippy 4.6.0
Show full stderr[06:53:57] This is snippy 4.6.0 [06:53:57] Written by Torsten Seemann [06:53:57] Obtained from https://github.com/tseemann/snippy [06:53:57] Detected operating system: linux [06:53:57] Enabling bundled linux tools. [06:53:57] Found bwa - /usr/local/bin/bwa [06:53:57] Found bcftools - /usr/local/bin/bcftools [06:53:57] Found samtools - /usr/local/bin/samtools [06:53:57] Found java - /usr/local/bin/java [06:53:57] Found snpEff - /usr/local/bin/snpEff [06:53:57] Found samclip - /usr/local/bin/samclip [06:53:57] Found seqtk - /usr/local/bin/seqtk [06:53:57] Found parallel - /usr/local/bin/parallel [06:53:57] Found freebayes - /usr/local/bin/freebayes [06:53:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:53:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:53:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:53:57] Found vcfuniq - /usr/local/bin/vcfuniq [06:53:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:53:57] Found gzip - /bin/gzip [06:53:57] Found vt - /usr/local/bin/vt [06:53:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:53:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:53:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:53:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:53:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:53:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:53:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:53:58] Please supply a reference FASTA/GBK/EMBL file with --reference
2[06:56:12] This is snippy 4.6.0
Show full stderr[06:56:12] This is snippy 4.6.0 [06:56:12] Written by Torsten Seemann [06:56:12] Obtained from https://github.com/tseemann/snippy [06:56:12] Detected operating system: linux [06:56:12] Enabling bundled linux tools. [06:56:12] Found bwa - /usr/local/bin/bwa [06:56:12] Found bcftools - /usr/local/bin/bcftools [06:56:12] Found samtools - /usr/local/bin/samtools [06:56:12] Found java - /usr/local/bin/java [06:56:12] Found snpEff - /usr/local/bin/snpEff [06:56:12] Found samclip - /usr/local/bin/samclip [06:56:12] Found seqtk - /usr/local/bin/seqtk [06:56:12] Found parallel - /usr/local/bin/parallel [06:56:12] Found freebayes - /usr/local/bin/freebayes [06:56:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:56:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:56:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:56:12] Found vcfuniq - /usr/local/bin/vcfuniq [06:56:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:56:12] Found gzip - /bin/gzip [06:56:12] Found vt - /usr/local/bin/vt [06:56:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:56:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:56:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:56:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:56:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:56:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:56:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:56:13] Please supply a reference FASTA/GBK/EMBL file with --reference
2[06:58:03] This is snippy 4.6.0
Show full stderr[06:58:03] This is snippy 4.6.0 [06:58:03] Written by Torsten Seemann [06:58:03] Obtained from https://github.com/tseemann/snippy [06:58:03] Detected operating system: linux [06:58:03] Enabling bundled linux tools. [06:58:03] Found bwa - /usr/local/bin/bwa [06:58:03] Found bcftools - /usr/local/bin/bcftools [06:58:03] Found samtools - /usr/local/bin/samtools [06:58:03] Found java - /usr/local/bin/java [06:58:03] Found snpEff - /usr/local/bin/snpEff [06:58:04] Found samclip - /usr/local/bin/samclip [06:58:04] Found seqtk - /usr/local/bin/seqtk [06:58:04] Found parallel - /usr/local/bin/parallel [06:58:04] Found freebayes - /usr/local/bin/freebayes [06:58:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:58:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:58:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:58:04] Found vcfuniq - /usr/local/bin/vcfuniq [06:58:04] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:58:04] Found gzip - /bin/gzip [06:58:04] Found vt - /usr/local/bin/vt [06:58:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:58:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:58:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:58:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:58:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:58:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:58:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:58:04] Please supply a reference FASTA/GBK/EMBL file with --reference
2[06:58:28] This is snippy 4.6.0
Show full stderr[06:58:28] This is snippy 4.6.0 [06:58:28] Written by Torsten Seemann [06:58:28] Obtained from https://github.com/tseemann/snippy [06:58:28] Detected operating system: linux [06:58:28] Enabling bundled linux tools. [06:58:28] Found bwa - /usr/local/bin/bwa [06:58:28] Found bcftools - /usr/local/bin/bcftools [06:58:28] Found samtools - /usr/local/bin/samtools [06:58:28] Found java - /usr/local/bin/java [06:58:28] Found snpEff - /usr/local/bin/snpEff [06:58:28] Found samclip - /usr/local/bin/samclip [06:58:28] Found seqtk - /usr/local/bin/seqtk [06:58:28] Found parallel - /usr/local/bin/parallel [06:58:28] Found freebayes - /usr/local/bin/freebayes [06:58:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:58:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:58:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:58:28] Found vcfuniq - /usr/local/bin/vcfuniq [06:58:28] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:58:28] Found gzip - /bin/gzip [06:58:28] Found vt - /usr/local/bin/vt [06:58:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:58:29] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:58:29] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:58:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:58:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:58:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:58:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:58:29] Please supply a reference FASTA/GBK/EMBL file with --reference
2[08:28:50] This is snippy 4.6.0
Show full stderr[08:28:50] This is snippy 4.6.0 [08:28:50] Written by Torsten Seemann [08:28:50] Obtained from https://github.com/tseemann/snippy [08:28:50] Detected operating system: linux [08:28:50] Enabling bundled linux tools. [08:28:50] Found bwa - /usr/local/bin/bwa [08:28:50] Found bcftools - /usr/local/bin/bcftools [08:28:50] Found samtools - /usr/local/bin/samtools [08:28:50] Found java - /usr/local/bin/java [08:28:50] Found snpEff - /usr/local/bin/snpEff [08:28:50] Found samclip - /usr/local/bin/samclip [08:28:50] Found seqtk - /usr/local/bin/seqtk [08:28:50] Found parallel - /usr/local/bin/parallel [08:28:50] Found freebayes - /usr/local/bin/freebayes [08:28:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:28:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:28:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:28:50] Found vcfuniq - /usr/local/bin/vcfuniq [08:28:50] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:28:50] Found gzip - /bin/gzip [08:28:50] Found vt - /usr/local/bin/vt [08:28:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:28:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:28:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:28:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:28:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:28:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:28:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:28:51] Please supply a reference FASTA/GBK/EMBL file with --reference
2[06:55:37] This is snippy 4.6.0
Show full stderr[06:55:37] This is snippy 4.6.0 [06:55:37] Written by Torsten Seemann [06:55:37] Obtained from https://github.com/tseemann/snippy [06:55:37] Detected operating system: linux [06:55:37] Enabling bundled linux tools. [06:55:37] Found bwa - /usr/local/bin/bwa [06:55:37] Found bcftools - /usr/local/bin/bcftools [06:55:37] Found samtools - /usr/local/bin/samtools [06:55:37] Found java - /usr/local/bin/java [06:55:37] Found snpEff - /usr/local/bin/snpEff [06:55:37] Found samclip - /usr/local/bin/samclip [06:55:37] Found seqtk - /usr/local/bin/seqtk [06:55:37] Found parallel - /usr/local/bin/parallel [06:55:37] Found freebayes - /usr/local/bin/freebayes [06:55:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:55:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:55:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:55:37] Found vcfuniq - /usr/local/bin/vcfuniq [06:55:37] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:55:37] Found gzip - /bin/gzip [06:55:37] Found vt - /usr/local/bin/vt [06:55:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:55:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:55:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:55:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:55:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:55:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:55:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:55:38] Please supply a reference FASTA/GBK/EMBL file with --reference
2[06:55:22] This is snippy 4.6.0
Show full stderr[06:55:22] This is snippy 4.6.0 [06:55:22] Written by Torsten Seemann [06:55:22] Obtained from https://github.com/tseemann/snippy [06:55:22] Detected operating system: linux [06:55:22] Enabling bundled linux tools. [06:55:22] Found bwa - /usr/local/bin/bwa [06:55:22] Found bcftools - /usr/local/bin/bcftools [06:55:22] Found samtools - /usr/local/bin/samtools [06:55:22] Found java - /usr/local/bin/java [06:55:22] Found snpEff - /usr/local/bin/snpEff [06:55:22] Found samclip - /usr/local/bin/samclip [06:55:22] Found seqtk - /usr/local/bin/seqtk [06:55:22] Found parallel - /usr/local/bin/parallel [06:55:22] Found freebayes - /usr/local/bin/freebayes [06:55:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:55:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:55:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:55:22] Found vcfuniq - /usr/local/bin/vcfuniq [06:55:22] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:55:22] Found gzip - /bin/gzip [06:55:22] Found vt - /usr/local/bin/vt [06:55:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:55:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:55:23] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:55:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:55:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:55:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:55:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:55:23] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:39:11] This is snippy 4.6.0
Show full stderr[07:39:11] This is snippy 4.6.0 [07:39:11] Written by Torsten Seemann [07:39:11] Obtained from https://github.com/tseemann/snippy [07:39:11] Detected operating system: linux [07:39:11] Enabling bundled linux tools. [07:39:11] Found bwa - /usr/local/bin/bwa [07:39:11] Found bcftools - /usr/local/bin/bcftools [07:39:11] Found samtools - /usr/local/bin/samtools [07:39:11] Found java - /usr/local/bin/java [07:39:11] Found snpEff - /usr/local/bin/snpEff [07:39:11] Found samclip - /usr/local/bin/samclip [07:39:11] Found seqtk - /usr/local/bin/seqtk [07:39:11] Found parallel - /usr/local/bin/parallel [07:39:11] Found freebayes - /usr/local/bin/freebayes [07:39:11] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:39:11] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:39:11] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:39:11] Found vcfuniq - /usr/local/bin/vcfuniq [07:39:11] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:39:11] Found gzip - /bin/gzip [07:39:11] Found vt - /usr/local/bin/vt [07:39:11] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:39:11] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:39:11] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:39:11] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:39:11] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:39:12] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:39:12] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:39:12] Please supply a reference FASTA/GBK/EMBL file with --reference
2[06:55:49] This is snippy 4.6.0
Show full stderr[06:55:49] This is snippy 4.6.0 [06:55:49] Written by Torsten Seemann [06:55:49] Obtained from https://github.com/tseemann/snippy [06:55:49] Detected operating system: linux [06:55:49] Enabling bundled linux tools. [06:55:49] Found bwa - /usr/local/bin/bwa [06:55:49] Found bcftools - /usr/local/bin/bcftools [06:55:49] Found samtools - /usr/local/bin/samtools [06:55:49] Found java - /usr/local/bin/java [06:55:49] Found snpEff - /usr/local/bin/snpEff [06:55:49] Found samclip - /usr/local/bin/samclip [06:55:49] Found seqtk - /usr/local/bin/seqtk [06:55:49] Found parallel - /usr/local/bin/parallel [06:55:49] Found freebayes - /usr/local/bin/freebayes [06:55:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:55:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:55:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:55:49] Found vcfuniq - /usr/local/bin/vcfuniq [06:55:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:55:49] Found gzip - /bin/gzip [06:55:49] Found vt - /usr/local/bin/vt [06:55:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:55:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:55:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:55:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:55:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:55:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:55:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:55:50] Please supply a reference FASTA/GBK/EMBL file with --reference
2[06:55:58] This is snippy 4.6.0
Show full stderr[06:55:58] This is snippy 4.6.0 [06:55:58] Written by Torsten Seemann [06:55:58] Obtained from https://github.com/tseemann/snippy [06:55:58] Detected operating system: linux [06:55:58] Enabling bundled linux tools. [06:55:58] Found bwa - /usr/local/bin/bwa [06:55:58] Found bcftools - /usr/local/bin/bcftools [06:55:58] Found samtools - /usr/local/bin/samtools [06:55:58] Found java - /usr/local/bin/java [06:55:58] Found snpEff - /usr/local/bin/snpEff [06:55:58] Found samclip - /usr/local/bin/samclip [06:55:58] Found seqtk - /usr/local/bin/seqtk [06:55:58] Found parallel - /usr/local/bin/parallel [06:55:58] Found freebayes - /usr/local/bin/freebayes [06:55:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:55:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:55:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:55:58] Found vcfuniq - /usr/local/bin/vcfuniq [06:55:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:55:58] Found gzip - /bin/gzip [06:55:58] Found vt - /usr/local/bin/vt [06:55:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:55:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:55:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:55:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:55:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:55:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:55:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:55:59] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:00:25] This is snippy 4.6.0
Show full stderr[07:00:25] This is snippy 4.6.0 [07:00:25] Written by Torsten Seemann [07:00:25] Obtained from https://github.com/tseemann/snippy [07:00:25] Detected operating system: linux [07:00:25] Enabling bundled linux tools. [07:00:25] Found bwa - /usr/local/bin/bwa [07:00:25] Found bcftools - /usr/local/bin/bcftools [07:00:25] Found samtools - /usr/local/bin/samtools [07:00:25] Found java - /usr/local/bin/java [07:00:25] Found snpEff - /usr/local/bin/snpEff [07:00:25] Found samclip - /usr/local/bin/samclip [07:00:25] Found seqtk - /usr/local/bin/seqtk [07:00:25] Found parallel - /usr/local/bin/parallel [07:00:25] Found freebayes - /usr/local/bin/freebayes [07:00:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:00:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:00:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:00:25] Found vcfuniq - /usr/local/bin/vcfuniq [07:00:25] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:00:25] Found gzip - /bin/gzip [07:00:25] Found vt - /usr/local/bin/vt [07:00:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:00:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:00:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:00:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:00:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:00:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:00:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:00:26] Please supply a reference FASTA/GBK/EMBL file with --reference
2[06:59:55] This is snippy 4.6.0
Show full stderr[06:59:55] This is snippy 4.6.0 [06:59:55] Written by Torsten Seemann [06:59:55] Obtained from https://github.com/tseemann/snippy [06:59:55] Detected operating system: linux [06:59:55] Enabling bundled linux tools. [06:59:55] Found bwa - /usr/local/bin/bwa [06:59:55] Found bcftools - /usr/local/bin/bcftools [06:59:55] Found samtools - /usr/local/bin/samtools [06:59:55] Found java - /usr/local/bin/java [06:59:55] Found snpEff - /usr/local/bin/snpEff [06:59:55] Found samclip - /usr/local/bin/samclip [06:59:55] Found seqtk - /usr/local/bin/seqtk [06:59:55] Found parallel - /usr/local/bin/parallel [06:59:55] Found freebayes - /usr/local/bin/freebayes [06:59:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:59:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:59:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:59:55] Found vcfuniq - /usr/local/bin/vcfuniq [06:59:55] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:59:55] Found gzip - /bin/gzip [06:59:55] Found vt - /usr/local/bin/vt [06:59:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:59:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:59:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:59:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:59:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:59:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:59:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:59:55] Please supply a reference FASTA/GBK/EMBL file with --reference
2[06:58:57] This is snippy 4.6.0
Show full stderr[06:58:57] This is snippy 4.6.0 [06:58:57] Written by Torsten Seemann [06:58:57] Obtained from https://github.com/tseemann/snippy [06:58:57] Detected operating system: linux [06:58:57] Enabling bundled linux tools. [06:58:58] Found bwa - /usr/local/bin/bwa [06:58:58] Found bcftools - /usr/local/bin/bcftools [06:58:58] Found samtools - /usr/local/bin/samtools [06:58:58] Found java - /usr/local/bin/java [06:58:58] Found snpEff - /usr/local/bin/snpEff [06:58:58] Found samclip - /usr/local/bin/samclip [06:58:58] Found seqtk - /usr/local/bin/seqtk [06:58:58] Found parallel - /usr/local/bin/parallel [06:58:58] Found freebayes - /usr/local/bin/freebayes [06:58:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:58:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:58:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:58:58] Found vcfuniq - /usr/local/bin/vcfuniq [06:58:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:58:58] Found gzip - /bin/gzip [06:58:58] Found vt - /usr/local/bin/vt [06:58:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:58:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:58:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:58:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:58:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:58:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:58:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:58:58] Please supply a reference FASTA/GBK/EMBL file with --reference
2[06:59:43] This is snippy 4.6.0
Show full stderr[06:59:43] This is snippy 4.6.0 [06:59:43] Written by Torsten Seemann [06:59:43] Obtained from https://github.com/tseemann/snippy [06:59:43] Detected operating system: linux [06:59:43] Enabling bundled linux tools. [06:59:43] Found bwa - /usr/local/bin/bwa [06:59:43] Found bcftools - /usr/local/bin/bcftools [06:59:43] Found samtools - /usr/local/bin/samtools [06:59:43] Found java - /usr/local/bin/java [06:59:43] Found snpEff - /usr/local/bin/snpEff [06:59:43] Found samclip - /usr/local/bin/samclip [06:59:43] Found seqtk - /usr/local/bin/seqtk [06:59:43] Found parallel - /usr/local/bin/parallel [06:59:43] Found freebayes - /usr/local/bin/freebayes [06:59:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:59:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:59:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:59:43] Found vcfuniq - /usr/local/bin/vcfuniq [06:59:43] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:59:43] Found gzip - /bin/gzip [06:59:43] Found vt - /usr/local/bin/vt [06:59:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:59:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:59:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:59:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:59:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:59:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:59:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:59:43] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:00:40] This is snippy 4.6.0
Show full stderr[07:00:40] This is snippy 4.6.0 [07:00:40] Written by Torsten Seemann [07:00:40] Obtained from https://github.com/tseemann/snippy [07:00:40] Detected operating system: linux [07:00:40] Enabling bundled linux tools. [07:00:40] Found bwa - /usr/local/bin/bwa [07:00:40] Found bcftools - /usr/local/bin/bcftools [07:00:40] Found samtools - /usr/local/bin/samtools [07:00:40] Found java - /usr/local/bin/java [07:00:40] Found snpEff - /usr/local/bin/snpEff [07:00:40] Found samclip - /usr/local/bin/samclip [07:00:40] Found seqtk - /usr/local/bin/seqtk [07:00:40] Found parallel - /usr/local/bin/parallel [07:00:40] Found freebayes - /usr/local/bin/freebayes [07:00:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:00:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:00:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:00:40] Found vcfuniq - /usr/local/bin/vcfuniq [07:00:40] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:00:40] Found gzip - /bin/gzip [07:00:40] Found vt - /usr/local/bin/vt [07:00:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:00:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:00:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:00:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:00:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:00:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:00:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:00:40] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:02:44] This is snippy 4.6.0
Show full stderr[07:02:44] This is snippy 4.6.0 [07:02:44] Written by Torsten Seemann [07:02:44] Obtained from https://github.com/tseemann/snippy [07:02:44] Detected operating system: linux [07:02:44] Enabling bundled linux tools. [07:02:44] Found bwa - /usr/local/bin/bwa [07:02:44] Found bcftools - /usr/local/bin/bcftools [07:02:44] Found samtools - /usr/local/bin/samtools [07:02:44] Found java - /usr/local/bin/java [07:02:44] Found snpEff - /usr/local/bin/snpEff [07:02:44] Found samclip - /usr/local/bin/samclip [07:02:44] Found seqtk - /usr/local/bin/seqtk [07:02:44] Found parallel - /usr/local/bin/parallel [07:02:44] Found freebayes - /usr/local/bin/freebayes [07:02:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:02:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:02:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:02:44] Found vcfuniq - /usr/local/bin/vcfuniq [07:02:44] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:02:44] Found gzip - /bin/gzip [07:02:44] Found vt - /usr/local/bin/vt [07:02:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:02:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:02:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:02:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:02:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:02:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:02:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:02:45] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:04:10] This is snippy 4.6.0
Show full stderr[07:04:10] This is snippy 4.6.0 [07:04:10] Written by Torsten Seemann [07:04:10] Obtained from https://github.com/tseemann/snippy [07:04:10] Detected operating system: linux [07:04:10] Enabling bundled linux tools. [07:04:10] Found bwa - /usr/local/bin/bwa [07:04:10] Found bcftools - /usr/local/bin/bcftools [07:04:10] Found samtools - /usr/local/bin/samtools [07:04:10] Found java - /usr/local/bin/java [07:04:10] Found snpEff - /usr/local/bin/snpEff [07:04:10] Found samclip - /usr/local/bin/samclip [07:04:10] Found seqtk - /usr/local/bin/seqtk [07:04:10] Found parallel - /usr/local/bin/parallel [07:04:10] Found freebayes - /usr/local/bin/freebayes [07:04:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:04:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:04:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:04:10] Found vcfuniq - /usr/local/bin/vcfuniq [07:04:10] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:04:10] Found gzip - /bin/gzip [07:04:10] Found vt - /usr/local/bin/vt [07:04:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:04:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:04:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:04:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:04:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:04:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:04:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:04:11] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:05:07] This is snippy 4.6.0
Show full stderr[07:05:07] This is snippy 4.6.0 [07:05:07] Written by Torsten Seemann [07:05:07] Obtained from https://github.com/tseemann/snippy [07:05:07] Detected operating system: linux [07:05:07] Enabling bundled linux tools. [07:05:07] Found bwa - /usr/local/bin/bwa [07:05:07] Found bcftools - /usr/local/bin/bcftools [07:05:07] Found samtools - /usr/local/bin/samtools [07:05:07] Found java - /usr/local/bin/java [07:05:07] Found snpEff - /usr/local/bin/snpEff [07:05:07] Found samclip - /usr/local/bin/samclip [07:05:07] Found seqtk - /usr/local/bin/seqtk [07:05:07] Found parallel - /usr/local/bin/parallel [07:05:07] Found freebayes - /usr/local/bin/freebayes [07:05:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:05:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:05:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:05:07] Found vcfuniq - /usr/local/bin/vcfuniq [07:05:07] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:05:07] Found gzip - /bin/gzip [07:05:07] Found vt - /usr/local/bin/vt [07:05:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:05:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:05:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:05:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:05:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:05:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:05:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:05:08] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:02:57] This is snippy 4.6.0
Show full stderr[07:02:57] This is snippy 4.6.0 [07:02:57] Written by Torsten Seemann [07:02:57] Obtained from https://github.com/tseemann/snippy [07:02:57] Detected operating system: linux [07:02:57] Enabling bundled linux tools. [07:02:57] Found bwa - /usr/local/bin/bwa [07:02:57] Found bcftools - /usr/local/bin/bcftools [07:02:57] Found samtools - /usr/local/bin/samtools [07:02:57] Found java - /usr/local/bin/java [07:02:57] Found snpEff - /usr/local/bin/snpEff [07:02:57] Found samclip - /usr/local/bin/samclip [07:02:57] Found seqtk - /usr/local/bin/seqtk [07:02:57] Found parallel - /usr/local/bin/parallel [07:02:57] Found freebayes - /usr/local/bin/freebayes [07:02:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:02:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:02:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:02:57] Found vcfuniq - /usr/local/bin/vcfuniq [07:02:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:02:57] Found gzip - /bin/gzip [07:02:57] Found vt - /usr/local/bin/vt [07:02:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:02:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:02:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:02:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:02:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:02:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:02:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:02:58] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:03:10] This is snippy 4.6.0
Show full stderr[07:03:10] This is snippy 4.6.0 [07:03:10] Written by Torsten Seemann [07:03:10] Obtained from https://github.com/tseemann/snippy [07:03:10] Detected operating system: linux [07:03:10] Enabling bundled linux tools. [07:03:10] Found bwa - /usr/local/bin/bwa [07:03:10] Found bcftools - /usr/local/bin/bcftools [07:03:10] Found samtools - /usr/local/bin/samtools [07:03:10] Found java - /usr/local/bin/java [07:03:10] Found snpEff - /usr/local/bin/snpEff [07:03:10] Found samclip - /usr/local/bin/samclip [07:03:10] Found seqtk - /usr/local/bin/seqtk [07:03:10] Found parallel - /usr/local/bin/parallel [07:03:10] Found freebayes - /usr/local/bin/freebayes [07:03:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:03:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:03:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:03:10] Found vcfuniq - /usr/local/bin/vcfuniq [07:03:10] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:03:10] Found gzip - /bin/gzip [07:03:10] Found vt - /usr/local/bin/vt [07:03:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:03:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:03:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:03:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:03:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:03:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:03:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:03:11] Please supply a reference FASTA/GBK/EMBL file with --reference
2[08:34:50] This is snippy 4.6.0
Show full stderr[08:34:50] This is snippy 4.6.0 [08:34:50] Written by Torsten Seemann [08:34:50] Obtained from https://github.com/tseemann/snippy [08:34:50] Detected operating system: linux [08:34:50] Enabling bundled linux tools. [08:34:50] Found bwa - /usr/local/bin/bwa [08:34:50] Found bcftools - /usr/local/bin/bcftools [08:34:50] Found samtools - /usr/local/bin/samtools [08:34:50] Found java - /usr/local/bin/java [08:34:50] Found snpEff - /usr/local/bin/snpEff [08:34:50] Found samclip - /usr/local/bin/samclip [08:34:50] Found seqtk - /usr/local/bin/seqtk [08:34:50] Found parallel - /usr/local/bin/parallel [08:34:50] Found freebayes - /usr/local/bin/freebayes [08:34:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:34:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:34:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:34:50] Found vcfuniq - /usr/local/bin/vcfuniq [08:34:50] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:34:50] Found gzip - /bin/gzip [08:34:50] Found vt - /usr/local/bin/vt [08:34:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:34:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:34:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:34:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:34:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:34:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:34:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:34:51] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:03:55] This is snippy 4.6.0
Show full stderr[07:03:55] This is snippy 4.6.0 [07:03:55] Written by Torsten Seemann [07:03:55] Obtained from https://github.com/tseemann/snippy [07:03:55] Detected operating system: linux [07:03:55] Enabling bundled linux tools. [07:03:55] Found bwa - /usr/local/bin/bwa [07:03:55] Found bcftools - /usr/local/bin/bcftools [07:03:55] Found samtools - /usr/local/bin/samtools [07:03:55] Found java - /usr/local/bin/java [07:03:55] Found snpEff - /usr/local/bin/snpEff [07:03:55] Found samclip - /usr/local/bin/samclip [07:03:55] Found seqtk - /usr/local/bin/seqtk [07:03:55] Found parallel - /usr/local/bin/parallel [07:03:55] Found freebayes - /usr/local/bin/freebayes [07:03:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:03:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:03:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:03:55] Found vcfuniq - /usr/local/bin/vcfuniq [07:03:55] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:03:55] Found gzip - /bin/gzip [07:03:55] Found vt - /usr/local/bin/vt [07:03:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:03:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:03:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:03:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:03:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:03:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:03:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:03:56] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:04:25] This is snippy 4.6.0
Show full stderr[07:04:25] This is snippy 4.6.0 [07:04:25] Written by Torsten Seemann [07:04:25] Obtained from https://github.com/tseemann/snippy [07:04:25] Detected operating system: linux [07:04:25] Enabling bundled linux tools. [07:04:25] Found bwa - /usr/local/bin/bwa [07:04:25] Found bcftools - /usr/local/bin/bcftools [07:04:25] Found samtools - /usr/local/bin/samtools [07:04:25] Found java - /usr/local/bin/java [07:04:25] Found snpEff - /usr/local/bin/snpEff [07:04:25] Found samclip - /usr/local/bin/samclip [07:04:25] Found seqtk - /usr/local/bin/seqtk [07:04:25] Found parallel - /usr/local/bin/parallel [07:04:25] Found freebayes - /usr/local/bin/freebayes [07:04:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:04:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:04:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:04:25] Found vcfuniq - /usr/local/bin/vcfuniq [07:04:25] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:04:25] Found gzip - /bin/gzip [07:04:25] Found vt - /usr/local/bin/vt [07:04:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:04:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:04:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:04:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:04:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:04:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:04:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:04:26] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:05:32] This is snippy 4.6.0
Show full stderr[07:05:32] This is snippy 4.6.0 [07:05:32] Written by Torsten Seemann [07:05:32] Obtained from https://github.com/tseemann/snippy [07:05:32] Detected operating system: linux [07:05:32] Enabling bundled linux tools. [07:05:32] Found bwa - /usr/local/bin/bwa [07:05:32] Found bcftools - /usr/local/bin/bcftools [07:05:32] Found samtools - /usr/local/bin/samtools [07:05:32] Found java - /usr/local/bin/java [07:05:32] Found snpEff - /usr/local/bin/snpEff [07:05:32] Found samclip - /usr/local/bin/samclip [07:05:32] Found seqtk - /usr/local/bin/seqtk [07:05:32] Found parallel - /usr/local/bin/parallel [07:05:32] Found freebayes - /usr/local/bin/freebayes [07:05:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:05:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:05:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:05:32] Found vcfuniq - /usr/local/bin/vcfuniq [07:05:32] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:05:32] Found gzip - /bin/gzip [07:05:32] Found vt - /usr/local/bin/vt [07:05:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:05:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:05:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:05:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:05:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:05:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:05:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:05:33] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:06:10] This is snippy 4.6.0
Show full stderr[07:06:10] This is snippy 4.6.0 [07:06:10] Written by Torsten Seemann [07:06:10] Obtained from https://github.com/tseemann/snippy [07:06:10] Detected operating system: linux [07:06:10] Enabling bundled linux tools. [07:06:10] Found bwa - /usr/local/bin/bwa [07:06:10] Found bcftools - /usr/local/bin/bcftools [07:06:10] Found samtools - /usr/local/bin/samtools [07:06:10] Found java - /usr/local/bin/java [07:06:10] Found snpEff - /usr/local/bin/snpEff [07:06:10] Found samclip - /usr/local/bin/samclip [07:06:10] Found seqtk - /usr/local/bin/seqtk [07:06:10] Found parallel - /usr/local/bin/parallel [07:06:10] Found freebayes - /usr/local/bin/freebayes [07:06:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:06:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:06:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:06:10] Found vcfuniq - /usr/local/bin/vcfuniq [07:06:10] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:06:10] Found gzip - /bin/gzip [07:06:10] Found vt - /usr/local/bin/vt [07:06:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:06:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:06:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:06:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:06:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:06:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:06:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:06:11] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:06:32] This is snippy 4.6.0
Show full stderr[07:06:32] This is snippy 4.6.0 [07:06:32] Written by Torsten Seemann [07:06:32] Obtained from https://github.com/tseemann/snippy [07:06:32] Detected operating system: linux [07:06:32] Enabling bundled linux tools. [07:06:32] Found bwa - /usr/local/bin/bwa [07:06:32] Found bcftools - /usr/local/bin/bcftools [07:06:32] Found samtools - /usr/local/bin/samtools [07:06:32] Found java - /usr/local/bin/java [07:06:32] Found snpEff - /usr/local/bin/snpEff [07:06:32] Found samclip - /usr/local/bin/samclip [07:06:32] Found seqtk - /usr/local/bin/seqtk [07:06:32] Found parallel - /usr/local/bin/parallel [07:06:32] Found freebayes - /usr/local/bin/freebayes [07:06:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:06:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:06:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:06:32] Found vcfuniq - /usr/local/bin/vcfuniq [07:06:32] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:06:32] Found gzip - /bin/gzip [07:06:32] Found vt - /usr/local/bin/vt [07:06:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:06:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:06:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:06:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:06:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:06:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:06:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:06:33] Please supply a reference FASTA/GBK/EMBL file with --reference
2[08:40:48] This is snippy 4.6.0
Show full stderr[08:40:48] This is snippy 4.6.0 [08:40:48] Written by Torsten Seemann [08:40:48] Obtained from https://github.com/tseemann/snippy [08:40:48] Detected operating system: linux [08:40:48] Enabling bundled linux tools. [08:40:48] Found bwa - /usr/local/bin/bwa [08:40:48] Found bcftools - /usr/local/bin/bcftools [08:40:48] Found samtools - /usr/local/bin/samtools [08:40:48] Found java - /usr/local/bin/java [08:40:48] Found snpEff - /usr/local/bin/snpEff [08:40:48] Found samclip - /usr/local/bin/samclip [08:40:48] Found seqtk - /usr/local/bin/seqtk [08:40:48] Found parallel - /usr/local/bin/parallel [08:40:48] Found freebayes - /usr/local/bin/freebayes [08:40:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:40:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:40:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:40:48] Found vcfuniq - /usr/local/bin/vcfuniq [08:40:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:40:48] Found gzip - /bin/gzip [08:40:48] Found vt - /usr/local/bin/vt [08:40:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:40:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:40:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:40:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:40:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:40:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:40:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:40:48] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:07:38] This is snippy 4.6.0
Show full stderr[07:07:38] This is snippy 4.6.0 [07:07:38] Written by Torsten Seemann [07:07:38] Obtained from https://github.com/tseemann/snippy [07:07:38] Detected operating system: linux [07:07:38] Enabling bundled linux tools. [07:07:38] Found bwa - /usr/local/bin/bwa [07:07:38] Found bcftools - /usr/local/bin/bcftools [07:07:38] Found samtools - /usr/local/bin/samtools [07:07:38] Found java - /usr/local/bin/java [07:07:38] Found snpEff - /usr/local/bin/snpEff [07:07:38] Found samclip - /usr/local/bin/samclip [07:07:38] Found seqtk - /usr/local/bin/seqtk [07:07:38] Found parallel - /usr/local/bin/parallel [07:07:38] Found freebayes - /usr/local/bin/freebayes [07:07:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:07:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:07:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:07:38] Found vcfuniq - /usr/local/bin/vcfuniq [07:07:38] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:07:38] Found gzip - /bin/gzip [07:07:38] Found vt - /usr/local/bin/vt [07:07:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:07:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:07:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:07:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:07:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:07:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:07:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:07:39] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:08:57] This is snippy 4.6.0
Show full stderr[07:08:57] This is snippy 4.6.0 [07:08:57] Written by Torsten Seemann [07:08:57] Obtained from https://github.com/tseemann/snippy [07:08:57] Detected operating system: linux [07:08:57] Enabling bundled linux tools. [07:08:57] Found bwa - /usr/local/bin/bwa [07:08:57] Found bcftools - /usr/local/bin/bcftools [07:08:57] Found samtools - /usr/local/bin/samtools [07:08:57] Found java - /usr/local/bin/java [07:08:57] Found snpEff - /usr/local/bin/snpEff [07:08:57] Found samclip - /usr/local/bin/samclip [07:08:57] Found seqtk - /usr/local/bin/seqtk [07:08:57] Found parallel - /usr/local/bin/parallel [07:08:57] Found freebayes - /usr/local/bin/freebayes [07:08:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:08:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:08:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:08:57] Found vcfuniq - /usr/local/bin/vcfuniq [07:08:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:08:57] Found gzip - /bin/gzip [07:08:57] Found vt - /usr/local/bin/vt [07:08:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:08:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:08:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:08:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:08:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:08:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:08:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:08:58] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:06:59] This is snippy 4.6.0
Show full stderr[07:06:59] This is snippy 4.6.0 [07:06:59] Written by Torsten Seemann [07:06:59] Obtained from https://github.com/tseemann/snippy [07:06:59] Detected operating system: linux [07:06:59] Enabling bundled linux tools. [07:06:59] Found bwa - /usr/local/bin/bwa [07:06:59] Found bcftools - /usr/local/bin/bcftools [07:06:59] Found samtools - /usr/local/bin/samtools [07:06:59] Found java - /usr/local/bin/java [07:06:59] Found snpEff - /usr/local/bin/snpEff [07:06:59] Found samclip - /usr/local/bin/samclip [07:06:59] Found seqtk - /usr/local/bin/seqtk [07:06:59] Found parallel - /usr/local/bin/parallel [07:06:59] Found freebayes - /usr/local/bin/freebayes [07:06:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:06:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:06:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:06:59] Found vcfuniq - /usr/local/bin/vcfuniq [07:06:59] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:06:59] Found gzip - /bin/gzip [07:06:59] Found vt - /usr/local/bin/vt [07:06:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:06:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:06:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:06:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:06:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:07:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:07:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:07:00] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:08:19] This is snippy 4.6.0
Show full stderr[07:08:19] This is snippy 4.6.0 [07:08:19] Written by Torsten Seemann [07:08:19] Obtained from https://github.com/tseemann/snippy [07:08:19] Detected operating system: linux [07:08:19] Enabling bundled linux tools. [07:08:19] Found bwa - /usr/local/bin/bwa [07:08:19] Found bcftools - /usr/local/bin/bcftools [07:08:19] Found samtools - /usr/local/bin/samtools [07:08:19] Found java - /usr/local/bin/java [07:08:19] Found snpEff - /usr/local/bin/snpEff [07:08:19] Found samclip - /usr/local/bin/samclip [07:08:19] Found seqtk - /usr/local/bin/seqtk [07:08:19] Found parallel - /usr/local/bin/parallel [07:08:19] Found freebayes - /usr/local/bin/freebayes [07:08:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:08:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:08:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:08:19] Found vcfuniq - /usr/local/bin/vcfuniq [07:08:19] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:08:19] Found gzip - /bin/gzip [07:08:19] Found vt - /usr/local/bin/vt [07:08:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:08:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:08:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:08:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:08:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:08:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:08:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:08:20] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:09:11] This is snippy 4.6.0
Show full stderr[07:09:11] This is snippy 4.6.0 [07:09:11] Written by Torsten Seemann [07:09:11] Obtained from https://github.com/tseemann/snippy [07:09:11] Detected operating system: linux [07:09:11] Enabling bundled linux tools. [07:09:11] Found bwa - /usr/local/bin/bwa [07:09:11] Found bcftools - /usr/local/bin/bcftools [07:09:11] Found samtools - /usr/local/bin/samtools [07:09:11] Found java - /usr/local/bin/java [07:09:11] Found snpEff - /usr/local/bin/snpEff [07:09:11] Found samclip - /usr/local/bin/samclip [07:09:11] Found seqtk - /usr/local/bin/seqtk [07:09:11] Found parallel - /usr/local/bin/parallel [07:09:11] Found freebayes - /usr/local/bin/freebayes [07:09:11] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:09:11] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:09:11] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:09:11] Found vcfuniq - /usr/local/bin/vcfuniq [07:09:11] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:09:11] Found gzip - /bin/gzip [07:09:11] Found vt - /usr/local/bin/vt [07:09:11] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:09:11] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:09:11] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:09:11] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:09:11] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:09:12] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:09:12] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:09:12] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:09:17] This is snippy 4.6.0
Show full stderr[07:09:17] This is snippy 4.6.0 [07:09:17] Written by Torsten Seemann [07:09:17] Obtained from https://github.com/tseemann/snippy [07:09:17] Detected operating system: linux [07:09:17] Enabling bundled linux tools. [07:09:17] Found bwa - /usr/local/bin/bwa [07:09:17] Found bcftools - /usr/local/bin/bcftools [07:09:17] Found samtools - /usr/local/bin/samtools [07:09:17] Found java - /usr/local/bin/java [07:09:17] Found snpEff - /usr/local/bin/snpEff [07:09:17] Found samclip - /usr/local/bin/samclip [07:09:17] Found seqtk - /usr/local/bin/seqtk [07:09:17] Found parallel - /usr/local/bin/parallel [07:09:17] Found freebayes - /usr/local/bin/freebayes [07:09:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:09:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:09:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:09:17] Found vcfuniq - /usr/local/bin/vcfuniq [07:09:17] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:09:17] Found gzip - /bin/gzip [07:09:17] Found vt - /usr/local/bin/vt [07:09:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:09:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:09:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:09:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:09:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:09:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:09:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:09:18] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:15:35] This is snippy 4.6.0
Show full stderr[07:15:35] This is snippy 4.6.0 [07:15:35] Written by Torsten Seemann [07:15:35] Obtained from https://github.com/tseemann/snippy [07:15:35] Detected operating system: linux [07:15:35] Enabling bundled linux tools. [07:15:35] Found bwa - /usr/local/bin/bwa [07:15:35] Found bcftools - /usr/local/bin/bcftools [07:15:35] Found samtools - /usr/local/bin/samtools [07:15:35] Found java - /usr/local/bin/java [07:15:35] Found snpEff - /usr/local/bin/snpEff [07:15:35] Found samclip - /usr/local/bin/samclip [07:15:35] Found seqtk - /usr/local/bin/seqtk [07:15:35] Found parallel - /usr/local/bin/parallel [07:15:35] Found freebayes - /usr/local/bin/freebayes [07:15:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:15:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:15:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:15:35] Found vcfuniq - /usr/local/bin/vcfuniq [07:15:35] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:15:35] Found gzip - /bin/gzip [07:15:35] Found vt - /usr/local/bin/vt [07:15:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:15:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:15:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:15:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:15:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:15:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:15:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:15:36] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:08:31] This is snippy 4.6.0
Show full stderr[07:08:31] This is snippy 4.6.0 [07:08:31] Written by Torsten Seemann [07:08:31] Obtained from https://github.com/tseemann/snippy [07:08:31] Detected operating system: linux [07:08:31] Enabling bundled linux tools. [07:08:31] Found bwa - /usr/local/bin/bwa [07:08:31] Found bcftools - /usr/local/bin/bcftools [07:08:31] Found samtools - /usr/local/bin/samtools [07:08:31] Found java - /usr/local/bin/java [07:08:31] Found snpEff - /usr/local/bin/snpEff [07:08:31] Found samclip - /usr/local/bin/samclip [07:08:31] Found seqtk - /usr/local/bin/seqtk [07:08:31] Found parallel - /usr/local/bin/parallel [07:08:31] Found freebayes - /usr/local/bin/freebayes [07:08:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:08:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:08:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:08:31] Found vcfuniq - /usr/local/bin/vcfuniq [07:08:31] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:08:31] Found gzip - /bin/gzip [07:08:31] Found vt - /usr/local/bin/vt [07:08:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:08:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:08:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:08:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:08:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:08:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:08:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:08:32] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:08:44] This is snippy 4.6.0
Show full stderr[07:08:44] This is snippy 4.6.0 [07:08:44] Written by Torsten Seemann [07:08:44] Obtained from https://github.com/tseemann/snippy [07:08:44] Detected operating system: linux [07:08:44] Enabling bundled linux tools. [07:08:44] Found bwa - /usr/local/bin/bwa [07:08:44] Found bcftools - /usr/local/bin/bcftools [07:08:44] Found samtools - /usr/local/bin/samtools [07:08:44] Found java - /usr/local/bin/java [07:08:44] Found snpEff - /usr/local/bin/snpEff [07:08:44] Found samclip - /usr/local/bin/samclip [07:08:44] Found seqtk - /usr/local/bin/seqtk [07:08:44] Found parallel - /usr/local/bin/parallel [07:08:44] Found freebayes - /usr/local/bin/freebayes [07:08:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:08:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:08:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:08:44] Found vcfuniq - /usr/local/bin/vcfuniq [07:08:44] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:08:44] Found gzip - /bin/gzip [07:08:44] Found vt - /usr/local/bin/vt [07:08:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:08:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:08:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:08:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:08:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:08:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:08:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:08:45] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:09:32] This is snippy 4.6.0
Show full stderr[07:09:32] This is snippy 4.6.0 [07:09:32] Written by Torsten Seemann [07:09:32] Obtained from https://github.com/tseemann/snippy [07:09:32] Detected operating system: linux [07:09:32] Enabling bundled linux tools. [07:09:32] Found bwa - /usr/local/bin/bwa [07:09:32] Found bcftools - /usr/local/bin/bcftools [07:09:32] Found samtools - /usr/local/bin/samtools [07:09:32] Found java - /usr/local/bin/java [07:09:32] Found snpEff - /usr/local/bin/snpEff [07:09:32] Found samclip - /usr/local/bin/samclip [07:09:32] Found seqtk - /usr/local/bin/seqtk [07:09:32] Found parallel - /usr/local/bin/parallel [07:09:32] Found freebayes - /usr/local/bin/freebayes [07:09:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:09:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:09:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:09:32] Found vcfuniq - /usr/local/bin/vcfuniq [07:09:32] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:09:32] Found gzip - /bin/gzip [07:09:32] Found vt - /usr/local/bin/vt [07:09:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:09:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:09:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:09:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:09:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:09:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:09:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:09:33] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:05:51] This is snippy 4.6.0
Show full stderr[07:05:51] This is snippy 4.6.0 [07:05:51] Written by Torsten Seemann [07:05:51] Obtained from https://github.com/tseemann/snippy [07:05:51] Detected operating system: linux [07:05:51] Enabling bundled linux tools. [07:05:51] Found bwa - /usr/local/bin/bwa [07:05:51] Found bcftools - /usr/local/bin/bcftools [07:05:51] Found samtools - /usr/local/bin/samtools [07:05:51] Found java - /usr/local/bin/java [07:05:51] Found snpEff - /usr/local/bin/snpEff [07:05:51] Found samclip - /usr/local/bin/samclip [07:05:51] Found seqtk - /usr/local/bin/seqtk [07:05:51] Found parallel - /usr/local/bin/parallel [07:05:51] Found freebayes - /usr/local/bin/freebayes [07:05:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:05:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:05:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:05:51] Found vcfuniq - /usr/local/bin/vcfuniq [07:05:51] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:05:51] Found gzip - /bin/gzip [07:05:51] Found vt - /usr/local/bin/vt [07:05:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:05:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:05:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:05:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:05:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:05:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:05:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:05:52] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:06:44] This is snippy 4.6.0
Show full stderr[07:06:44] This is snippy 4.6.0 [07:06:44] Written by Torsten Seemann [07:06:44] Obtained from https://github.com/tseemann/snippy [07:06:44] Detected operating system: linux [07:06:44] Enabling bundled linux tools. [07:06:44] Found bwa - /usr/local/bin/bwa [07:06:44] Found bcftools - /usr/local/bin/bcftools [07:06:44] Found samtools - /usr/local/bin/samtools [07:06:44] Found java - /usr/local/bin/java [07:06:44] Found snpEff - /usr/local/bin/snpEff [07:06:44] Found samclip - /usr/local/bin/samclip [07:06:44] Found seqtk - /usr/local/bin/seqtk [07:06:44] Found parallel - /usr/local/bin/parallel [07:06:44] Found freebayes - /usr/local/bin/freebayes [07:06:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:06:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:06:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:06:44] Found vcfuniq - /usr/local/bin/vcfuniq [07:06:44] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:06:44] Found gzip - /bin/gzip [07:06:44] Found vt - /usr/local/bin/vt [07:06:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:06:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:06:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:06:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:06:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:06:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:06:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:06:45] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:11:49] This is snippy 4.6.0
Show full stderr[07:11:49] This is snippy 4.6.0 [07:11:49] Written by Torsten Seemann [07:11:49] Obtained from https://github.com/tseemann/snippy [07:11:49] Detected operating system: linux [07:11:49] Enabling bundled linux tools. [07:11:49] Found bwa - /usr/local/bin/bwa [07:11:49] Found bcftools - /usr/local/bin/bcftools [07:11:49] Found samtools - /usr/local/bin/samtools [07:11:49] Found java - /usr/local/bin/java [07:11:49] Found snpEff - /usr/local/bin/snpEff [07:11:49] Found samclip - /usr/local/bin/samclip [07:11:49] Found seqtk - /usr/local/bin/seqtk [07:11:49] Found parallel - /usr/local/bin/parallel [07:11:49] Found freebayes - /usr/local/bin/freebayes [07:11:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:11:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:11:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:11:49] Found vcfuniq - /usr/local/bin/vcfuniq [07:11:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:11:49] Found gzip - /bin/gzip [07:11:49] Found vt - /usr/local/bin/vt [07:11:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:11:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:11:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:11:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:11:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:11:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:11:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:11:50] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:12:06] This is snippy 4.6.0
Show full stderr[07:12:06] This is snippy 4.6.0 [07:12:06] Written by Torsten Seemann [07:12:06] Obtained from https://github.com/tseemann/snippy [07:12:06] Detected operating system: linux [07:12:06] Enabling bundled linux tools. [07:12:06] Found bwa - /usr/local/bin/bwa [07:12:06] Found bcftools - /usr/local/bin/bcftools [07:12:06] Found samtools - /usr/local/bin/samtools [07:12:06] Found java - /usr/local/bin/java [07:12:06] Found snpEff - /usr/local/bin/snpEff [07:12:06] Found samclip - /usr/local/bin/samclip [07:12:06] Found seqtk - /usr/local/bin/seqtk [07:12:06] Found parallel - /usr/local/bin/parallel [07:12:06] Found freebayes - /usr/local/bin/freebayes [07:12:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:12:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:12:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:12:06] Found vcfuniq - /usr/local/bin/vcfuniq [07:12:06] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:12:06] Found gzip - /bin/gzip [07:12:06] Found vt - /usr/local/bin/vt [07:12:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:12:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:12:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:12:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:12:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:12:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:12:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:12:07] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:12:17] This is snippy 4.6.0
Show full stderr[07:12:17] This is snippy 4.6.0 [07:12:17] Written by Torsten Seemann [07:12:17] Obtained from https://github.com/tseemann/snippy [07:12:17] Detected operating system: linux [07:12:17] Enabling bundled linux tools. [07:12:17] Found bwa - /usr/local/bin/bwa [07:12:17] Found bcftools - /usr/local/bin/bcftools [07:12:17] Found samtools - /usr/local/bin/samtools [07:12:17] Found java - /usr/local/bin/java [07:12:17] Found snpEff - /usr/local/bin/snpEff [07:12:17] Found samclip - /usr/local/bin/samclip [07:12:17] Found seqtk - /usr/local/bin/seqtk [07:12:17] Found parallel - /usr/local/bin/parallel [07:12:17] Found freebayes - /usr/local/bin/freebayes [07:12:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:12:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:12:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:12:17] Found vcfuniq - /usr/local/bin/vcfuniq [07:12:17] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:12:17] Found gzip - /bin/gzip [07:12:17] Found vt - /usr/local/bin/vt [07:12:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:12:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:12:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:12:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:12:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:12:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:12:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:12:18] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:12:58] This is snippy 4.6.0
Show full stderr[07:12:58] This is snippy 4.6.0 [07:12:58] Written by Torsten Seemann [07:12:58] Obtained from https://github.com/tseemann/snippy [07:12:58] Detected operating system: linux [07:12:58] Enabling bundled linux tools. [07:12:58] Found bwa - /usr/local/bin/bwa [07:12:58] Found bcftools - /usr/local/bin/bcftools [07:12:58] Found samtools - /usr/local/bin/samtools [07:12:58] Found java - /usr/local/bin/java [07:12:58] Found snpEff - /usr/local/bin/snpEff [07:12:58] Found samclip - /usr/local/bin/samclip [07:12:58] Found seqtk - /usr/local/bin/seqtk [07:12:58] Found parallel - /usr/local/bin/parallel [07:12:58] Found freebayes - /usr/local/bin/freebayes [07:12:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:12:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:12:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:12:58] Found vcfuniq - /usr/local/bin/vcfuniq [07:12:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:12:59] Found gzip - /bin/gzip [07:12:59] Found vt - /usr/local/bin/vt [07:12:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:12:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:12:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:12:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:12:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:12:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:12:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:12:59] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:11:38] This is snippy 4.6.0
Show full stderr[07:11:38] This is snippy 4.6.0 [07:11:38] Written by Torsten Seemann [07:11:38] Obtained from https://github.com/tseemann/snippy [07:11:38] Detected operating system: linux [07:11:38] Enabling bundled linux tools. [07:11:38] Found bwa - /usr/local/bin/bwa [07:11:38] Found bcftools - /usr/local/bin/bcftools [07:11:38] Found samtools - /usr/local/bin/samtools [07:11:38] Found java - /usr/local/bin/java [07:11:38] Found snpEff - /usr/local/bin/snpEff [07:11:38] Found samclip - /usr/local/bin/samclip [07:11:38] Found seqtk - /usr/local/bin/seqtk [07:11:38] Found parallel - /usr/local/bin/parallel [07:11:38] Found freebayes - /usr/local/bin/freebayes [07:11:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:11:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:11:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:11:38] Found vcfuniq - /usr/local/bin/vcfuniq [07:11:38] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:11:38] Found gzip - /bin/gzip [07:11:38] Found vt - /usr/local/bin/vt [07:11:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:11:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:11:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:11:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:11:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:11:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:11:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:11:39] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:12:03] This is snippy 4.6.0
Show full stderr[07:12:03] This is snippy 4.6.0 [07:12:03] Written by Torsten Seemann [07:12:03] Obtained from https://github.com/tseemann/snippy [07:12:03] Detected operating system: linux [07:12:03] Enabling bundled linux tools. [07:12:03] Found bwa - /usr/local/bin/bwa [07:12:03] Found bcftools - /usr/local/bin/bcftools [07:12:03] Found samtools - /usr/local/bin/samtools [07:12:03] Found java - /usr/local/bin/java [07:12:03] Found snpEff - /usr/local/bin/snpEff [07:12:03] Found samclip - /usr/local/bin/samclip [07:12:03] Found seqtk - /usr/local/bin/seqtk [07:12:03] Found parallel - /usr/local/bin/parallel [07:12:03] Found freebayes - /usr/local/bin/freebayes [07:12:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:12:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:12:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:12:03] Found vcfuniq - /usr/local/bin/vcfuniq [07:12:03] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:12:03] Found gzip - /bin/gzip [07:12:03] Found vt - /usr/local/bin/vt [07:12:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:12:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:12:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:12:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:12:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:12:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:12:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:12:04] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:11:53] This is snippy 4.6.0
Show full stderr[07:11:53] This is snippy 4.6.0 [07:11:53] Written by Torsten Seemann [07:11:53] Obtained from https://github.com/tseemann/snippy [07:11:53] Detected operating system: linux [07:11:53] Enabling bundled linux tools. [07:11:53] Found bwa - /usr/local/bin/bwa [07:11:53] Found bcftools - /usr/local/bin/bcftools [07:11:53] Found samtools - /usr/local/bin/samtools [07:11:53] Found java - /usr/local/bin/java [07:11:53] Found snpEff - /usr/local/bin/snpEff [07:11:53] Found samclip - /usr/local/bin/samclip [07:11:53] Found seqtk - /usr/local/bin/seqtk [07:11:53] Found parallel - /usr/local/bin/parallel [07:11:53] Found freebayes - /usr/local/bin/freebayes [07:11:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:11:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:11:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:11:53] Found vcfuniq - /usr/local/bin/vcfuniq [07:11:53] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:11:53] Found gzip - /bin/gzip [07:11:53] Found vt - /usr/local/bin/vt [07:11:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:11:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:11:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:11:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:11:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:11:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:11:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:11:54] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:12:46] This is snippy 4.6.0
Show full stderr[07:12:46] This is snippy 4.6.0 [07:12:46] Written by Torsten Seemann [07:12:46] Obtained from https://github.com/tseemann/snippy [07:12:46] Detected operating system: linux [07:12:46] Enabling bundled linux tools. [07:12:46] Found bwa - /usr/local/bin/bwa [07:12:46] Found bcftools - /usr/local/bin/bcftools [07:12:46] Found samtools - /usr/local/bin/samtools [07:12:46] Found java - /usr/local/bin/java [07:12:46] Found snpEff - /usr/local/bin/snpEff [07:12:46] Found samclip - /usr/local/bin/samclip [07:12:46] Found seqtk - /usr/local/bin/seqtk [07:12:46] Found parallel - /usr/local/bin/parallel [07:12:46] Found freebayes - /usr/local/bin/freebayes [07:12:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:12:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:12:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:12:46] Found vcfuniq - /usr/local/bin/vcfuniq [07:12:46] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:12:46] Found gzip - /bin/gzip [07:12:46] Found vt - /usr/local/bin/vt [07:12:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:12:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:12:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:12:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:12:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:12:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:12:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:12:47] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:13:12] This is snippy 4.6.0
Show full stderr[07:13:12] This is snippy 4.6.0 [07:13:12] Written by Torsten Seemann [07:13:12] Obtained from https://github.com/tseemann/snippy [07:13:12] Detected operating system: linux [07:13:12] Enabling bundled linux tools. [07:13:12] Found bwa - /usr/local/bin/bwa [07:13:12] Found bcftools - /usr/local/bin/bcftools [07:13:12] Found samtools - /usr/local/bin/samtools [07:13:12] Found java - /usr/local/bin/java [07:13:12] Found snpEff - /usr/local/bin/snpEff [07:13:12] Found samclip - /usr/local/bin/samclip [07:13:12] Found seqtk - /usr/local/bin/seqtk [07:13:12] Found parallel - /usr/local/bin/parallel [07:13:12] Found freebayes - /usr/local/bin/freebayes [07:13:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:13:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:13:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:13:13] Found vcfuniq - /usr/local/bin/vcfuniq [07:13:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:13:13] Found gzip - /bin/gzip [07:13:13] Found vt - /usr/local/bin/vt [07:13:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:13:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:13:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:13:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:13:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:13:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:13:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:13:13] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:16:02] This is snippy 4.6.0
Show full stderr[07:16:02] This is snippy 4.6.0 [07:16:02] Written by Torsten Seemann [07:16:02] Obtained from https://github.com/tseemann/snippy [07:16:02] Detected operating system: linux [07:16:02] Enabling bundled linux tools. [07:16:02] Found bwa - /usr/local/bin/bwa [07:16:02] Found bcftools - /usr/local/bin/bcftools [07:16:02] Found samtools - /usr/local/bin/samtools [07:16:02] Found java - /usr/local/bin/java [07:16:02] Found snpEff - /usr/local/bin/snpEff [07:16:02] Found samclip - /usr/local/bin/samclip [07:16:02] Found seqtk - /usr/local/bin/seqtk [07:16:02] Found parallel - /usr/local/bin/parallel [07:16:02] Found freebayes - /usr/local/bin/freebayes [07:16:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:16:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:16:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:16:02] Found vcfuniq - /usr/local/bin/vcfuniq [07:16:02] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:16:02] Found gzip - /bin/gzip [07:16:02] Found vt - /usr/local/bin/vt [07:16:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:16:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:16:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:16:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:16:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:16:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:16:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:16:03] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:15:49] This is snippy 4.6.0
Show full stderr[07:15:49] This is snippy 4.6.0 [07:15:49] Written by Torsten Seemann [07:15:49] Obtained from https://github.com/tseemann/snippy [07:15:49] Detected operating system: linux [07:15:49] Enabling bundled linux tools. [07:15:49] Found bwa - /usr/local/bin/bwa [07:15:49] Found bcftools - /usr/local/bin/bcftools [07:15:49] Found samtools - /usr/local/bin/samtools [07:15:49] Found java - /usr/local/bin/java [07:15:49] Found snpEff - /usr/local/bin/snpEff [07:15:49] Found samclip - /usr/local/bin/samclip [07:15:49] Found seqtk - /usr/local/bin/seqtk [07:15:49] Found parallel - /usr/local/bin/parallel [07:15:49] Found freebayes - /usr/local/bin/freebayes [07:15:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:15:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:15:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:15:49] Found vcfuniq - /usr/local/bin/vcfuniq [07:15:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:15:49] Found gzip - /bin/gzip [07:15:49] Found vt - /usr/local/bin/vt [07:15:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:15:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:15:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:15:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:15:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:15:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:15:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:15:50] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:26:09] This is snippy 4.6.0
Show full stderr[07:26:09] This is snippy 4.6.0 [07:26:09] Written by Torsten Seemann [07:26:09] Obtained from https://github.com/tseemann/snippy [07:26:09] Detected operating system: linux [07:26:09] Enabling bundled linux tools. [07:26:09] Found bwa - /usr/local/bin/bwa [07:26:09] Found bcftools - /usr/local/bin/bcftools [07:26:09] Found samtools - /usr/local/bin/samtools [07:26:09] Found java - /usr/local/bin/java [07:26:09] Found snpEff - /usr/local/bin/snpEff [07:26:09] Found samclip - /usr/local/bin/samclip [07:26:09] Found seqtk - /usr/local/bin/seqtk [07:26:09] Found parallel - /usr/local/bin/parallel [07:26:09] Found freebayes - /usr/local/bin/freebayes [07:26:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:26:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:26:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:26:09] Found vcfuniq - /usr/local/bin/vcfuniq [07:26:09] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:26:09] Found gzip - /bin/gzip [07:26:09] Found vt - /usr/local/bin/vt [07:26:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:26:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:26:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:26:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:26:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:26:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:26:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:26:10] Using reference: /corral4/main/objects/b/c/7/dataset_bc72f994-0ee8-49f5-b32a-d0eb5858fef9.dat [07:26:10] Treating reference as 'fasta' format. [07:26:10] Will use 1 CPU cores. [07:26:10] Using read file: /corral4/main/objects/b/9/3/dataset_b931e0c8-c97a-491e-9665-7515b51f803c.dat [07:26:10] Creating folder: BVBRC_genome_sequence___2025_10_25T135701_613_fasta [07:26:10] Changing working directory: BVBRC_genome_sequence___2025_10_25T135701_613_fasta [07:26:10] Creating reference folder: reference [07:26:10] Extracting FASTA and GFF from reference. [07:26:10] Wrote 1 sequences to ref.fa [07:26:10] Wrote 0 features to ref.gff [07:26:10] Shredding /corral4/main/objects/b/9/3/dataset_b931e0c8-c97a-491e-9665-7515b51f803c.dat into pseudo-reads [07:26:12] Wrote 219280 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [07:26:12] Freebayes will process 1 chunks of 2868471 bp, 1 chunks at a time. [07:26:12] Using BAM RG (Read Group) ID: BVBRC_genome_sequence___2025_10_25T135701_613_fasta [07:26:12] Running: samtools faidx reference/ref.fa 2>> snps.log [07:26:13] Running: bwa index reference/ref.fa 2>> snps.log [07:26:14] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [07:26:14] Running: ln -sf reference/ref.fa . 2>> snps.log [07:26:14] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [07:26:14] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [07:26:14] Running: bwa mem -Y -M -R '@RG\tID:BVBRC_genome_sequence___2025_10_25T135701_613_fasta\tSM:BVBRC_genome_sequence___2025_10_25T135701_613_fasta' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/263/72263194/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/263/72263194/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/263/72263194/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::process] read 19280 sequences (4820000 bp)... [M::mem_proc
2[07:26:12] This is snippy 4.6.0
Show full stderr[07:26:12] This is snippy 4.6.0 [07:26:12] Written by Torsten Seemann [07:26:12] Obtained from https://github.com/tseemann/snippy [07:26:12] Detected operating system: linux [07:26:12] Enabling bundled linux tools. [07:26:12] Found bwa - /usr/local/bin/bwa [07:26:12] Found bcftools - /usr/local/bin/bcftools [07:26:12] Found samtools - /usr/local/bin/samtools [07:26:12] Found java - /usr/local/bin/java [07:26:12] Found snpEff - /usr/local/bin/snpEff [07:26:12] Found samclip - /usr/local/bin/samclip [07:26:12] Found seqtk - /usr/local/bin/seqtk [07:26:12] Found parallel - /usr/local/bin/parallel [07:26:12] Found freebayes - /usr/local/bin/freebayes [07:26:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:26:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:26:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:26:13] Found vcfuniq - /usr/local/bin/vcfuniq [07:26:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:26:13] Found gzip - /bin/gzip [07:26:13] Found vt - /usr/local/bin/vt [07:26:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:26:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:26:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:26:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:26:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:26:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:26:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:26:13] Using reference: /corral4/main/objects/b/c/7/dataset_bc72f994-0ee8-49f5-b32a-d0eb5858fef9.dat [07:26:13] Treating reference as 'fasta' format. [07:26:13] Will use 1 CPU cores. [07:26:13] Using read file: /corral4/main/objects/f/9/1/dataset_f91c1dae-8edf-47ef-85e8-e7216580cbc0.dat [07:26:13] Creating folder: BVBRC_genome_sequence___2025_10_25T135718_903_fasta [07:26:13] Changing working directory: BVBRC_genome_sequence___2025_10_25T135718_903_fasta [07:26:13] Creating reference folder: reference [07:26:13] Extracting FASTA and GFF from reference. [07:26:13] Wrote 1 sequences to ref.fa [07:26:13] Wrote 0 features to ref.gff [07:26:13] Shredding /corral4/main/objects/f/9/1/dataset_f91c1dae-8edf-47ef-85e8-e7216580cbc0.dat into pseudo-reads [07:26:16] Wrote 221700 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [07:26:16] Freebayes will process 1 chunks of 2868471 bp, 1 chunks at a time. [07:26:16] Using BAM RG (Read Group) ID: BVBRC_genome_sequence___2025_10_25T135718_903_fasta [07:26:16] Running: samtools faidx reference/ref.fa 2>> snps.log [07:26:16] Running: bwa index reference/ref.fa 2>> snps.log [07:26:17] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [07:26:17] Running: ln -sf reference/ref.fa . 2>> snps.log [07:26:17] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [07:26:17] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [07:26:17] Running: bwa mem -Y -M -R '@RG\tID:BVBRC_genome_sequence___2025_10_25T135718_903_fasta\tSM:BVBRC_genome_sequence___2025_10_25T135718_903_fasta' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/263/72263198/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/263/72263198/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/263/72263198/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::process] read 21700 sequences (5425000 bp)... [M::mem_proc
2[07:28:56] This is snippy 4.6.0
Show full stderr[07:28:56] This is snippy 4.6.0 [07:28:56] Written by Torsten Seemann [07:28:56] Obtained from https://github.com/tseemann/snippy [07:28:56] Detected operating system: linux [07:28:56] Enabling bundled linux tools. [07:28:56] Found bwa - /usr/local/bin/bwa [07:28:56] Found bcftools - /usr/local/bin/bcftools [07:28:56] Found samtools - /usr/local/bin/samtools [07:28:56] Found java - /usr/local/bin/java [07:28:56] Found snpEff - /usr/local/bin/snpEff [07:28:56] Found samclip - /usr/local/bin/samclip [07:28:56] Found seqtk - /usr/local/bin/seqtk [07:28:56] Found parallel - /usr/local/bin/parallel [07:28:56] Found freebayes - /usr/local/bin/freebayes [07:28:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:28:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:28:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:28:56] Found vcfuniq - /usr/local/bin/vcfuniq [07:28:56] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:28:56] Found gzip - /bin/gzip [07:28:56] Found vt - /usr/local/bin/vt [07:28:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:28:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:28:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:28:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:28:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:28:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:28:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:28:57] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:29:25] This is snippy 4.6.0
Show full stderr[07:29:25] This is snippy 4.6.0 [07:29:25] Written by Torsten Seemann [07:29:25] Obtained from https://github.com/tseemann/snippy [07:29:25] Detected operating system: linux [07:29:25] Enabling bundled linux tools. [07:29:25] Found bwa - /usr/local/bin/bwa [07:29:25] Found bcftools - /usr/local/bin/bcftools [07:29:25] Found samtools - /usr/local/bin/samtools [07:29:25] Found java - /usr/local/bin/java [07:29:25] Found snpEff - /usr/local/bin/snpEff [07:29:25] Found samclip - /usr/local/bin/samclip [07:29:25] Found seqtk - /usr/local/bin/seqtk [07:29:25] Found parallel - /usr/local/bin/parallel [07:29:25] Found freebayes - /usr/local/bin/freebayes [07:29:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:29:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:29:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:29:25] Found vcfuniq - /usr/local/bin/vcfuniq [07:29:25] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:29:25] Found gzip - /bin/gzip [07:29:25] Found vt - /usr/local/bin/vt [07:29:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:29:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:29:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:29:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:29:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:29:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:29:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:29:26] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:30:40] This is snippy 4.6.0
Show full stderr[07:30:40] This is snippy 4.6.0 [07:30:40] Written by Torsten Seemann [07:30:40] Obtained from https://github.com/tseemann/snippy [07:30:40] Detected operating system: linux [07:30:40] Enabling bundled linux tools. [07:30:40] Found bwa - /usr/local/bin/bwa [07:30:40] Found bcftools - /usr/local/bin/bcftools [07:30:40] Found samtools - /usr/local/bin/samtools [07:30:40] Found java - /usr/local/bin/java [07:30:40] Found snpEff - /usr/local/bin/snpEff [07:30:40] Found samclip - /usr/local/bin/samclip [07:30:40] Found seqtk - /usr/local/bin/seqtk [07:30:40] Found parallel - /usr/local/bin/parallel [07:30:40] Found freebayes - /usr/local/bin/freebayes [07:30:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:30:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:30:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:30:40] Found vcfuniq - /usr/local/bin/vcfuniq [07:30:40] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:30:40] Found gzip - /bin/gzip [07:30:40] Found vt - /usr/local/bin/vt [07:30:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:30:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:30:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:30:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:30:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:30:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:30:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:30:41] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:30:57] This is snippy 4.6.0
Show full stderr[07:30:57] This is snippy 4.6.0 [07:30:57] Written by Torsten Seemann [07:30:57] Obtained from https://github.com/tseemann/snippy [07:30:57] Detected operating system: linux [07:30:57] Enabling bundled linux tools. [07:30:57] Found bwa - /usr/local/bin/bwa [07:30:57] Found bcftools - /usr/local/bin/bcftools [07:30:57] Found samtools - /usr/local/bin/samtools [07:30:57] Found java - /usr/local/bin/java [07:30:57] Found snpEff - /usr/local/bin/snpEff [07:30:57] Found samclip - /usr/local/bin/samclip [07:30:57] Found seqtk - /usr/local/bin/seqtk [07:30:57] Found parallel - /usr/local/bin/parallel [07:30:57] Found freebayes - /usr/local/bin/freebayes [07:30:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:30:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:30:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:30:57] Found vcfuniq - /usr/local/bin/vcfuniq [07:30:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:30:57] Found gzip - /bin/gzip [07:30:57] Found vt - /usr/local/bin/vt [07:30:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:30:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:30:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:30:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:30:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:30:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:30:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:30:58] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:31:10] This is snippy 4.6.0
Show full stderr[07:31:10] This is snippy 4.6.0 [07:31:10] Written by Torsten Seemann [07:31:10] Obtained from https://github.com/tseemann/snippy [07:31:10] Detected operating system: linux [07:31:10] Enabling bundled linux tools. [07:31:10] Found bwa - /usr/local/bin/bwa [07:31:10] Found bcftools - /usr/local/bin/bcftools [07:31:10] Found samtools - /usr/local/bin/samtools [07:31:10] Found java - /usr/local/bin/java [07:31:10] Found snpEff - /usr/local/bin/snpEff [07:31:10] Found samclip - /usr/local/bin/samclip [07:31:10] Found seqtk - /usr/local/bin/seqtk [07:31:10] Found parallel - /usr/local/bin/parallel [07:31:10] Found freebayes - /usr/local/bin/freebayes [07:31:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:31:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:31:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:31:10] Found vcfuniq - /usr/local/bin/vcfuniq [07:31:10] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:31:10] Found gzip - /bin/gzip [07:31:10] Found vt - /usr/local/bin/vt [07:31:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:31:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:31:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:31:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:31:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:31:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:31:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:31:11] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:28:41] This is snippy 4.6.0
Show full stderr[07:28:41] This is snippy 4.6.0 [07:28:41] Written by Torsten Seemann [07:28:41] Obtained from https://github.com/tseemann/snippy [07:28:41] Detected operating system: linux [07:28:41] Enabling bundled linux tools. [07:28:41] Found bwa - /usr/local/bin/bwa [07:28:41] Found bcftools - /usr/local/bin/bcftools [07:28:41] Found samtools - /usr/local/bin/samtools [07:28:41] Found java - /usr/local/bin/java [07:28:41] Found snpEff - /usr/local/bin/snpEff [07:28:41] Found samclip - /usr/local/bin/samclip [07:28:41] Found seqtk - /usr/local/bin/seqtk [07:28:41] Found parallel - /usr/local/bin/parallel [07:28:41] Found freebayes - /usr/local/bin/freebayes [07:28:41] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:28:41] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:28:41] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:28:41] Found vcfuniq - /usr/local/bin/vcfuniq [07:28:41] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:28:41] Found gzip - /bin/gzip [07:28:41] Found vt - /usr/local/bin/vt [07:28:41] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:28:41] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:28:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:28:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:28:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:28:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:28:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:28:42] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:28:16] This is snippy 4.6.0
Show full stderr[07:28:16] This is snippy 4.6.0 [07:28:16] Written by Torsten Seemann [07:28:16] Obtained from https://github.com/tseemann/snippy [07:28:16] Detected operating system: linux [07:28:16] Enabling bundled linux tools. [07:28:16] Found bwa - /usr/local/bin/bwa [07:28:16] Found bcftools - /usr/local/bin/bcftools [07:28:16] Found samtools - /usr/local/bin/samtools [07:28:16] Found java - /usr/local/bin/java [07:28:16] Found snpEff - /usr/local/bin/snpEff [07:28:16] Found samclip - /usr/local/bin/samclip [07:28:16] Found seqtk - /usr/local/bin/seqtk [07:28:16] Found parallel - /usr/local/bin/parallel [07:28:16] Found freebayes - /usr/local/bin/freebayes [07:28:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:28:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:28:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:28:16] Found vcfuniq - /usr/local/bin/vcfuniq [07:28:16] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:28:16] Found gzip - /bin/gzip [07:28:16] Found vt - /usr/local/bin/vt [07:28:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:28:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:28:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:28:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:28:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:28:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:28:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:28:17] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:28:32] This is snippy 4.6.0
Show full stderr[07:28:32] This is snippy 4.6.0 [07:28:32] Written by Torsten Seemann [07:28:32] Obtained from https://github.com/tseemann/snippy [07:28:32] Detected operating system: linux [07:28:32] Enabling bundled linux tools. [07:28:32] Found bwa - /usr/local/bin/bwa [07:28:32] Found bcftools - /usr/local/bin/bcftools [07:28:32] Found samtools - /usr/local/bin/samtools [07:28:32] Found java - /usr/local/bin/java [07:28:32] Found snpEff - /usr/local/bin/snpEff [07:28:32] Found samclip - /usr/local/bin/samclip [07:28:32] Found seqtk - /usr/local/bin/seqtk [07:28:32] Found parallel - /usr/local/bin/parallel [07:28:32] Found freebayes - /usr/local/bin/freebayes [07:28:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:28:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:28:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:28:32] Found vcfuniq - /usr/local/bin/vcfuniq [07:28:32] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:28:32] Found gzip - /bin/gzip [07:28:32] Found vt - /usr/local/bin/vt [07:28:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:28:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:28:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:28:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:28:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:28:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:28:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:28:32] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:29:10] This is snippy 4.6.0
Show full stderr[07:29:10] This is snippy 4.6.0 [07:29:10] Written by Torsten Seemann [07:29:10] Obtained from https://github.com/tseemann/snippy [07:29:10] Detected operating system: linux [07:29:10] Enabling bundled linux tools. [07:29:10] Found bwa - /usr/local/bin/bwa [07:29:10] Found bcftools - /usr/local/bin/bcftools [07:29:10] Found samtools - /usr/local/bin/samtools [07:29:10] Found java - /usr/local/bin/java [07:29:10] Found snpEff - /usr/local/bin/snpEff [07:29:10] Found samclip - /usr/local/bin/samclip [07:29:10] Found seqtk - /usr/local/bin/seqtk [07:29:10] Found parallel - /usr/local/bin/parallel [07:29:10] Found freebayes - /usr/local/bin/freebayes [07:29:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:29:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:29:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:29:10] Found vcfuniq - /usr/local/bin/vcfuniq [07:29:10] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:29:10] Found gzip - /bin/gzip [07:29:10] Found vt - /usr/local/bin/vt [07:29:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:29:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:29:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:29:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:29:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:29:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:29:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:29:11] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:29:46] This is snippy 4.6.0
Show full stderr[07:29:46] This is snippy 4.6.0 [07:29:46] Written by Torsten Seemann [07:29:46] Obtained from https://github.com/tseemann/snippy [07:29:46] Detected operating system: linux [07:29:46] Enabling bundled linux tools. [07:29:46] Found bwa - /usr/local/bin/bwa [07:29:46] Found bcftools - /usr/local/bin/bcftools [07:29:46] Found samtools - /usr/local/bin/samtools [07:29:46] Found java - /usr/local/bin/java [07:29:46] Found snpEff - /usr/local/bin/snpEff [07:29:46] Found samclip - /usr/local/bin/samclip [07:29:46] Found seqtk - /usr/local/bin/seqtk [07:29:46] Found parallel - /usr/local/bin/parallel [07:29:46] Found freebayes - /usr/local/bin/freebayes [07:29:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:29:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:29:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:29:46] Found vcfuniq - /usr/local/bin/vcfuniq [07:29:46] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:29:46] Found gzip - /bin/gzip [07:29:46] Found vt - /usr/local/bin/vt [07:29:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:29:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:29:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:29:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:29:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:29:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:29:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:29:47] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:28:44] This is snippy 4.6.0
Show full stderr[07:28:44] This is snippy 4.6.0 [07:28:44] Written by Torsten Seemann [07:28:44] Obtained from https://github.com/tseemann/snippy [07:28:44] Detected operating system: linux [07:28:44] Enabling bundled linux tools. [07:28:44] Found bwa - /usr/local/bin/bwa [07:28:44] Found bcftools - /usr/local/bin/bcftools [07:28:44] Found samtools - /usr/local/bin/samtools [07:28:44] Found java - /usr/local/bin/java [07:28:44] Found snpEff - /usr/local/bin/snpEff [07:28:44] Found samclip - /usr/local/bin/samclip [07:28:44] Found seqtk - /usr/local/bin/seqtk [07:28:44] Found parallel - /usr/local/bin/parallel [07:28:44] Found freebayes - /usr/local/bin/freebayes [07:28:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:28:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:28:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:28:44] Found vcfuniq - /usr/local/bin/vcfuniq [07:28:44] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:28:44] Found gzip - /bin/gzip [07:28:44] Found vt - /usr/local/bin/vt [07:28:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:28:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:28:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:28:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:28:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:28:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:28:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:28:44] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:31:34] This is snippy 4.6.0
Show full stderr[07:31:34] This is snippy 4.6.0 [07:31:34] Written by Torsten Seemann [07:31:34] Obtained from https://github.com/tseemann/snippy [07:31:34] Detected operating system: linux [07:31:34] Enabling bundled linux tools. [07:31:34] Found bwa - /usr/local/bin/bwa [07:31:34] Found bcftools - /usr/local/bin/bcftools [07:31:34] Found samtools - /usr/local/bin/samtools [07:31:34] Found java - /usr/local/bin/java [07:31:34] Found snpEff - /usr/local/bin/snpEff [07:31:34] Found samclip - /usr/local/bin/samclip [07:31:34] Found seqtk - /usr/local/bin/seqtk [07:31:34] Found parallel - /usr/local/bin/parallel [07:31:34] Found freebayes - /usr/local/bin/freebayes [07:31:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:31:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:31:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:31:34] Found vcfuniq - /usr/local/bin/vcfuniq [07:31:34] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:31:34] Found gzip - /bin/gzip [07:31:34] Found vt - /usr/local/bin/vt [07:31:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:31:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:31:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:31:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:31:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:31:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:31:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:31:35] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:33:56] This is snippy 4.6.0
Show full stderr[07:33:56] This is snippy 4.6.0 [07:33:56] Written by Torsten Seemann [07:33:56] Obtained from https://github.com/tseemann/snippy [07:33:56] Detected operating system: linux [07:33:56] Enabling bundled linux tools. [07:33:56] Found bwa - /usr/local/bin/bwa [07:33:56] Found bcftools - /usr/local/bin/bcftools [07:33:56] Found samtools - /usr/local/bin/samtools [07:33:56] Found java - /usr/local/bin/java [07:33:56] Found snpEff - /usr/local/bin/snpEff [07:33:56] Found samclip - /usr/local/bin/samclip [07:33:56] Found seqtk - /usr/local/bin/seqtk [07:33:56] Found parallel - /usr/local/bin/parallel [07:33:56] Found freebayes - /usr/local/bin/freebayes [07:33:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:33:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:33:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:33:56] Found vcfuniq - /usr/local/bin/vcfuniq [07:33:56] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:33:56] Found gzip - /bin/gzip [07:33:56] Found vt - /usr/local/bin/vt [07:33:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:33:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:33:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:33:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:33:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:33:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:33:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:33:57] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:33:59] This is snippy 4.6.0
Show full stderr[07:33:59] This is snippy 4.6.0 [07:33:59] Written by Torsten Seemann [07:33:59] Obtained from https://github.com/tseemann/snippy [07:33:59] Detected operating system: linux [07:33:59] Enabling bundled linux tools. [07:33:59] Found bwa - /usr/local/bin/bwa [07:33:59] Found bcftools - /usr/local/bin/bcftools [07:33:59] Found samtools - /usr/local/bin/samtools [07:33:59] Found java - /usr/local/bin/java [07:33:59] Found snpEff - /usr/local/bin/snpEff [07:33:59] Found samclip - /usr/local/bin/samclip [07:33:59] Found seqtk - /usr/local/bin/seqtk [07:33:59] Found parallel - /usr/local/bin/parallel [07:33:59] Found freebayes - /usr/local/bin/freebayes [07:33:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:33:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:33:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:33:59] Found vcfuniq - /usr/local/bin/vcfuniq [07:33:59] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:33:59] Found gzip - /bin/gzip [07:33:59] Found vt - /usr/local/bin/vt [07:33:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:33:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:33:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:33:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:33:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:34:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:34:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:34:00] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:30:31] This is snippy 4.6.0
Show full stderr[07:30:31] This is snippy 4.6.0 [07:30:31] Written by Torsten Seemann [07:30:31] Obtained from https://github.com/tseemann/snippy [07:30:31] Detected operating system: linux [07:30:31] Enabling bundled linux tools. [07:30:31] Found bwa - /usr/local/bin/bwa [07:30:31] Found bcftools - /usr/local/bin/bcftools [07:30:31] Found samtools - /usr/local/bin/samtools [07:30:31] Found java - /usr/local/bin/java [07:30:31] Found snpEff - /usr/local/bin/snpEff [07:30:31] Found samclip - /usr/local/bin/samclip [07:30:31] Found seqtk - /usr/local/bin/seqtk [07:30:31] Found parallel - /usr/local/bin/parallel [07:30:31] Found freebayes - /usr/local/bin/freebayes [07:30:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:30:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:30:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:30:31] Found vcfuniq - /usr/local/bin/vcfuniq [07:30:31] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:30:31] Found gzip - /bin/gzip [07:30:31] Found vt - /usr/local/bin/vt [07:30:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:30:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:30:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:30:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:30:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:30:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:30:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:30:32] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:34:37] This is snippy 4.6.0
Show full stderr[07:34:37] This is snippy 4.6.0 [07:34:37] Written by Torsten Seemann [07:34:37] Obtained from https://github.com/tseemann/snippy [07:34:37] Detected operating system: linux [07:34:37] Enabling bundled linux tools. [07:34:37] Found bwa - /usr/local/bin/bwa [07:34:37] Found bcftools - /usr/local/bin/bcftools [07:34:37] Found samtools - /usr/local/bin/samtools [07:34:37] Found java - /usr/local/bin/java [07:34:37] Found snpEff - /usr/local/bin/snpEff [07:34:37] Found samclip - /usr/local/bin/samclip [07:34:37] Found seqtk - /usr/local/bin/seqtk [07:34:37] Found parallel - /usr/local/bin/parallel [07:34:37] Found freebayes - /usr/local/bin/freebayes [07:34:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:34:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:34:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:34:37] Found vcfuniq - /usr/local/bin/vcfuniq [07:34:37] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:34:37] Found gzip - /bin/gzip [07:34:37] Found vt - /usr/local/bin/vt [07:34:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:34:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:34:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:34:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:34:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:34:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:34:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:34:38] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:35:04] This is snippy 4.6.0
Show full stderr[07:35:04] This is snippy 4.6.0 [07:35:04] Written by Torsten Seemann [07:35:04] Obtained from https://github.com/tseemann/snippy [07:35:04] Detected operating system: linux [07:35:04] Enabling bundled linux tools. [07:35:04] Found bwa - /usr/local/bin/bwa [07:35:04] Found bcftools - /usr/local/bin/bcftools [07:35:04] Found samtools - /usr/local/bin/samtools [07:35:04] Found java - /usr/local/bin/java [07:35:04] Found snpEff - /usr/local/bin/snpEff [07:35:04] Found samclip - /usr/local/bin/samclip [07:35:04] Found seqtk - /usr/local/bin/seqtk [07:35:04] Found parallel - /usr/local/bin/parallel [07:35:04] Found freebayes - /usr/local/bin/freebayes [07:35:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:35:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:35:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:35:04] Found vcfuniq - /usr/local/bin/vcfuniq [07:35:04] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:35:04] Found gzip - /bin/gzip [07:35:04] Found vt - /usr/local/bin/vt [07:35:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:35:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:35:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:35:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:35:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:35:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:35:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:35:05] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:35:33] This is snippy 4.6.0
Show full stderr[07:35:33] This is snippy 4.6.0 [07:35:33] Written by Torsten Seemann [07:35:33] Obtained from https://github.com/tseemann/snippy [07:35:33] Detected operating system: linux [07:35:33] Enabling bundled linux tools. [07:35:33] Found bwa - /usr/local/bin/bwa [07:35:33] Found bcftools - /usr/local/bin/bcftools [07:35:33] Found samtools - /usr/local/bin/samtools [07:35:33] Found java - /usr/local/bin/java [07:35:33] Found snpEff - /usr/local/bin/snpEff [07:35:33] Found samclip - /usr/local/bin/samclip [07:35:33] Found seqtk - /usr/local/bin/seqtk [07:35:33] Found parallel - /usr/local/bin/parallel [07:35:33] Found freebayes - /usr/local/bin/freebayes [07:35:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:35:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:35:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:35:33] Found vcfuniq - /usr/local/bin/vcfuniq [07:35:33] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:35:33] Found gzip - /bin/gzip [07:35:33] Found vt - /usr/local/bin/vt [07:35:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:35:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:35:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:35:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:35:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:35:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:35:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:35:34] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:32:39] This is snippy 4.6.0
Show full stderr[07:32:39] This is snippy 4.6.0 [07:32:39] Written by Torsten Seemann [07:32:39] Obtained from https://github.com/tseemann/snippy [07:32:39] Detected operating system: linux [07:32:39] Enabling bundled linux tools. [07:32:39] Found bwa - /usr/local/bin/bwa [07:32:39] Found bcftools - /usr/local/bin/bcftools [07:32:39] Found samtools - /usr/local/bin/samtools [07:32:39] Found java - /usr/local/bin/java [07:32:39] Found snpEff - /usr/local/bin/snpEff [07:32:39] Found samclip - /usr/local/bin/samclip [07:32:39] Found seqtk - /usr/local/bin/seqtk [07:32:39] Found parallel - /usr/local/bin/parallel [07:32:39] Found freebayes - /usr/local/bin/freebayes [07:32:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:32:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:32:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:32:39] Found vcfuniq - /usr/local/bin/vcfuniq [07:32:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:32:39] Found gzip - /bin/gzip [07:32:39] Found vt - /usr/local/bin/vt [07:32:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:32:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:32:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:32:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:32:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:32:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:32:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:32:40] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:32:51] This is snippy 4.6.0
Show full stderr[07:32:51] This is snippy 4.6.0 [07:32:51] Written by Torsten Seemann [07:32:51] Obtained from https://github.com/tseemann/snippy [07:32:51] Detected operating system: linux [07:32:51] Enabling bundled linux tools. [07:32:51] Found bwa - /usr/local/bin/bwa [07:32:51] Found bcftools - /usr/local/bin/bcftools [07:32:51] Found samtools - /usr/local/bin/samtools [07:32:51] Found java - /usr/local/bin/java [07:32:51] Found snpEff - /usr/local/bin/snpEff [07:32:51] Found samclip - /usr/local/bin/samclip [07:32:51] Found seqtk - /usr/local/bin/seqtk [07:32:51] Found parallel - /usr/local/bin/parallel [07:32:51] Found freebayes - /usr/local/bin/freebayes [07:32:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:32:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:32:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:32:51] Found vcfuniq - /usr/local/bin/vcfuniq [07:32:51] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:32:51] Found gzip - /bin/gzip [07:32:51] Found vt - /usr/local/bin/vt [07:32:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:32:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:32:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:32:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:32:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:32:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:32:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:32:52] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:32:54] This is snippy 4.6.0
Show full stderr[07:32:54] This is snippy 4.6.0 [07:32:54] Written by Torsten Seemann [07:32:54] Obtained from https://github.com/tseemann/snippy [07:32:54] Detected operating system: linux [07:32:54] Enabling bundled linux tools. [07:32:54] Found bwa - /usr/local/bin/bwa [07:32:54] Found bcftools - /usr/local/bin/bcftools [07:32:54] Found samtools - /usr/local/bin/samtools [07:32:54] Found java - /usr/local/bin/java [07:32:54] Found snpEff - /usr/local/bin/snpEff [07:32:54] Found samclip - /usr/local/bin/samclip [07:32:54] Found seqtk - /usr/local/bin/seqtk [07:32:54] Found parallel - /usr/local/bin/parallel [07:32:54] Found freebayes - /usr/local/bin/freebayes [07:32:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:32:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:32:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:32:54] Found vcfuniq - /usr/local/bin/vcfuniq [07:32:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:32:54] Found gzip - /bin/gzip [07:32:54] Found vt - /usr/local/bin/vt [07:32:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:32:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:32:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:32:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:32:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:32:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:32:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:32:55] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:35:19] This is snippy 4.6.0
Show full stderr[07:35:19] This is snippy 4.6.0 [07:35:19] Written by Torsten Seemann [07:35:19] Obtained from https://github.com/tseemann/snippy [07:35:19] Detected operating system: linux [07:35:19] Enabling bundled linux tools. [07:35:19] Found bwa - /usr/local/bin/bwa [07:35:19] Found bcftools - /usr/local/bin/bcftools [07:35:19] Found samtools - /usr/local/bin/samtools [07:35:19] Found java - /usr/local/bin/java [07:35:19] Found snpEff - /usr/local/bin/snpEff [07:35:19] Found samclip - /usr/local/bin/samclip [07:35:19] Found seqtk - /usr/local/bin/seqtk [07:35:19] Found parallel - /usr/local/bin/parallel [07:35:19] Found freebayes - /usr/local/bin/freebayes [07:35:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:35:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:35:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:35:19] Found vcfuniq - /usr/local/bin/vcfuniq [07:35:19] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:35:19] Found gzip - /bin/gzip [07:35:19] Found vt - /usr/local/bin/vt [07:35:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:35:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:35:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:35:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:35:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:35:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:35:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:35:20] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:36:47] This is snippy 4.6.0
Show full stderr[07:36:47] This is snippy 4.6.0 [07:36:47] Written by Torsten Seemann [07:36:47] Obtained from https://github.com/tseemann/snippy [07:36:47] Detected operating system: linux [07:36:47] Enabling bundled linux tools. [07:36:47] Found bwa - /usr/local/bin/bwa [07:36:47] Found bcftools - /usr/local/bin/bcftools [07:36:47] Found samtools - /usr/local/bin/samtools [07:36:47] Found java - /usr/local/bin/java [07:36:47] Found snpEff - /usr/local/bin/snpEff [07:36:47] Found samclip - /usr/local/bin/samclip [07:36:47] Found seqtk - /usr/local/bin/seqtk [07:36:47] Found parallel - /usr/local/bin/parallel [07:36:47] Found freebayes - /usr/local/bin/freebayes [07:36:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:36:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:36:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:36:47] Found vcfuniq - /usr/local/bin/vcfuniq [07:36:47] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:36:47] Found gzip - /bin/gzip [07:36:47] Found vt - /usr/local/bin/vt [07:36:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:36:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:36:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:36:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:36:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:36:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:36:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:36:48] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:37:02] This is snippy 4.6.0
Show full stderr[07:37:02] This is snippy 4.6.0 [07:37:02] Written by Torsten Seemann [07:37:02] Obtained from https://github.com/tseemann/snippy [07:37:02] Detected operating system: linux [07:37:02] Enabling bundled linux tools. [07:37:02] Found bwa - /usr/local/bin/bwa [07:37:02] Found bcftools - /usr/local/bin/bcftools [07:37:02] Found samtools - /usr/local/bin/samtools [07:37:02] Found java - /usr/local/bin/java [07:37:02] Found snpEff - /usr/local/bin/snpEff [07:37:02] Found samclip - /usr/local/bin/samclip [07:37:02] Found seqtk - /usr/local/bin/seqtk [07:37:02] Found parallel - /usr/local/bin/parallel [07:37:02] Found freebayes - /usr/local/bin/freebayes [07:37:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:37:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:37:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:37:02] Found vcfuniq - /usr/local/bin/vcfuniq [07:37:02] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:37:02] Found gzip - /bin/gzip [07:37:02] Found vt - /usr/local/bin/vt [07:37:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:37:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:37:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:37:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:37:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:37:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:37:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:37:03] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:37:16] This is snippy 4.6.0
Show full stderr[07:37:16] This is snippy 4.6.0 [07:37:16] Written by Torsten Seemann [07:37:16] Obtained from https://github.com/tseemann/snippy [07:37:16] Detected operating system: linux [07:37:16] Enabling bundled linux tools. [07:37:16] Found bwa - /usr/local/bin/bwa [07:37:16] Found bcftools - /usr/local/bin/bcftools [07:37:16] Found samtools - /usr/local/bin/samtools [07:37:16] Found java - /usr/local/bin/java [07:37:16] Found snpEff - /usr/local/bin/snpEff [07:37:16] Found samclip - /usr/local/bin/samclip [07:37:16] Found seqtk - /usr/local/bin/seqtk [07:37:16] Found parallel - /usr/local/bin/parallel [07:37:16] Found freebayes - /usr/local/bin/freebayes [07:37:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:37:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:37:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:37:16] Found vcfuniq - /usr/local/bin/vcfuniq [07:37:16] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:37:16] Found gzip - /bin/gzip [07:37:16] Found vt - /usr/local/bin/vt [07:37:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:37:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:37:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:37:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:37:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:37:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:37:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:37:17] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:37:28] This is snippy 4.6.0
Show full stderr[07:37:28] This is snippy 4.6.0 [07:37:28] Written by Torsten Seemann [07:37:28] Obtained from https://github.com/tseemann/snippy [07:37:28] Detected operating system: linux [07:37:28] Enabling bundled linux tools. [07:37:28] Found bwa - /usr/local/bin/bwa [07:37:28] Found bcftools - /usr/local/bin/bcftools [07:37:28] Found samtools - /usr/local/bin/samtools [07:37:28] Found java - /usr/local/bin/java [07:37:28] Found snpEff - /usr/local/bin/snpEff [07:37:28] Found samclip - /usr/local/bin/samclip [07:37:28] Found seqtk - /usr/local/bin/seqtk [07:37:28] Found parallel - /usr/local/bin/parallel [07:37:28] Found freebayes - /usr/local/bin/freebayes [07:37:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:37:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:37:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:37:28] Found vcfuniq - /usr/local/bin/vcfuniq [07:37:28] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:37:28] Found gzip - /bin/gzip [07:37:28] Found vt - /usr/local/bin/vt [07:37:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:37:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:37:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:37:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:37:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:37:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:37:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:37:29] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:39:50] This is snippy 4.6.0
Show full stderr[07:39:50] This is snippy 4.6.0 [07:39:50] Written by Torsten Seemann [07:39:50] Obtained from https://github.com/tseemann/snippy [07:39:50] Detected operating system: linux [07:39:50] Enabling bundled linux tools. [07:39:50] Found bwa - /usr/local/bin/bwa [07:39:50] Found bcftools - /usr/local/bin/bcftools [07:39:50] Found samtools - /usr/local/bin/samtools [07:39:50] Found java - /usr/local/bin/java [07:39:50] Found snpEff - /usr/local/bin/snpEff [07:39:50] Found samclip - /usr/local/bin/samclip [07:39:50] Found seqtk - /usr/local/bin/seqtk [07:39:50] Found parallel - /usr/local/bin/parallel [07:39:51] Found freebayes - /usr/local/bin/freebayes [07:39:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:39:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:39:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:39:51] Found vcfuniq - /usr/local/bin/vcfuniq [07:39:51] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:39:51] Found gzip - /bin/gzip [07:39:51] Found vt - /usr/local/bin/vt [07:39:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:39:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:39:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:39:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:39:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:39:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:39:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:39:51] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:33:04] This is snippy 4.6.0
Show full stderr[07:33:04] This is snippy 4.6.0 [07:33:04] Written by Torsten Seemann [07:33:04] Obtained from https://github.com/tseemann/snippy [07:33:04] Detected operating system: linux [07:33:04] Enabling bundled linux tools. [07:33:04] Found bwa - /usr/local/bin/bwa [07:33:04] Found bcftools - /usr/local/bin/bcftools [07:33:04] Found samtools - /usr/local/bin/samtools [07:33:04] Found java - /usr/local/bin/java [07:33:04] Found snpEff - /usr/local/bin/snpEff [07:33:04] Found samclip - /usr/local/bin/samclip [07:33:04] Found seqtk - /usr/local/bin/seqtk [07:33:04] Found parallel - /usr/local/bin/parallel [07:33:04] Found freebayes - /usr/local/bin/freebayes [07:33:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:33:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:33:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:33:04] Found vcfuniq - /usr/local/bin/vcfuniq [07:33:04] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:33:04] Found gzip - /bin/gzip [07:33:04] Found vt - /usr/local/bin/vt [07:33:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:33:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:33:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:33:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:33:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:33:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:33:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:33:05] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:35:39] This is snippy 4.6.0
Show full stderr[07:35:39] This is snippy 4.6.0 [07:35:39] Written by Torsten Seemann [07:35:39] Obtained from https://github.com/tseemann/snippy [07:35:39] Detected operating system: linux [07:35:39] Enabling bundled linux tools. [07:35:39] Found bwa - /usr/local/bin/bwa [07:35:39] Found bcftools - /usr/local/bin/bcftools [07:35:39] Found samtools - /usr/local/bin/samtools [07:35:39] Found java - /usr/local/bin/java [07:35:39] Found snpEff - /usr/local/bin/snpEff [07:35:39] Found samclip - /usr/local/bin/samclip [07:35:39] Found seqtk - /usr/local/bin/seqtk [07:35:39] Found parallel - /usr/local/bin/parallel [07:35:39] Found freebayes - /usr/local/bin/freebayes [07:35:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:35:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:35:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:35:39] Found vcfuniq - /usr/local/bin/vcfuniq [07:35:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:35:39] Found gzip - /bin/gzip [07:35:39] Found vt - /usr/local/bin/vt [07:35:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:35:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:35:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:35:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:35:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:35:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:35:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:35:40] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:36:34] This is snippy 4.6.0
Show full stderr[07:36:34] This is snippy 4.6.0 [07:36:34] Written by Torsten Seemann [07:36:34] Obtained from https://github.com/tseemann/snippy [07:36:34] Detected operating system: linux [07:36:34] Enabling bundled linux tools. [07:36:34] Found bwa - /usr/local/bin/bwa [07:36:34] Found bcftools - /usr/local/bin/bcftools [07:36:34] Found samtools - /usr/local/bin/samtools [07:36:34] Found java - /usr/local/bin/java [07:36:34] Found snpEff - /usr/local/bin/snpEff [07:36:34] Found samclip - /usr/local/bin/samclip [07:36:34] Found seqtk - /usr/local/bin/seqtk [07:36:34] Found parallel - /usr/local/bin/parallel [07:36:34] Found freebayes - /usr/local/bin/freebayes [07:36:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:36:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:36:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:36:34] Found vcfuniq - /usr/local/bin/vcfuniq [07:36:34] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:36:34] Found gzip - /bin/gzip [07:36:34] Found vt - /usr/local/bin/vt [07:36:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:36:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:36:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:36:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:36:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:36:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:36:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:36:35] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:38:25] This is snippy 4.6.0
Show full stderr[07:38:25] This is snippy 4.6.0 [07:38:25] Written by Torsten Seemann [07:38:25] Obtained from https://github.com/tseemann/snippy [07:38:25] Detected operating system: linux [07:38:25] Enabling bundled linux tools. [07:38:25] Found bwa - /usr/local/bin/bwa [07:38:25] Found bcftools - /usr/local/bin/bcftools [07:38:25] Found samtools - /usr/local/bin/samtools [07:38:25] Found java - /usr/local/bin/java [07:38:25] Found snpEff - /usr/local/bin/snpEff [07:38:25] Found samclip - /usr/local/bin/samclip [07:38:25] Found seqtk - /usr/local/bin/seqtk [07:38:25] Found parallel - /usr/local/bin/parallel [07:38:25] Found freebayes - /usr/local/bin/freebayes [07:38:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:38:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:38:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:38:25] Found vcfuniq - /usr/local/bin/vcfuniq [07:38:25] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:38:25] Found gzip - /bin/gzip [07:38:25] Found vt - /usr/local/bin/vt [07:38:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:38:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:38:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:38:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:38:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:38:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:38:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:38:26] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:40:21] This is snippy 4.6.0
Show full stderr[07:40:21] This is snippy 4.6.0 [07:40:21] Written by Torsten Seemann [07:40:21] Obtained from https://github.com/tseemann/snippy [07:40:21] Detected operating system: linux [07:40:21] Enabling bundled linux tools. [07:40:21] Found bwa - /usr/local/bin/bwa [07:40:21] Found bcftools - /usr/local/bin/bcftools [07:40:21] Found samtools - /usr/local/bin/samtools [07:40:21] Found java - /usr/local/bin/java [07:40:21] Found snpEff - /usr/local/bin/snpEff [07:40:22] Found samclip - /usr/local/bin/samclip [07:40:22] Found seqtk - /usr/local/bin/seqtk [07:40:22] Found parallel - /usr/local/bin/parallel [07:40:22] Found freebayes - /usr/local/bin/freebayes [07:40:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:40:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:40:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:40:22] Found vcfuniq - /usr/local/bin/vcfuniq [07:40:22] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:40:22] Found gzip - /bin/gzip [07:40:22] Found vt - /usr/local/bin/vt [07:40:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:40:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:40:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:40:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:40:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:40:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:40:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:40:22] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:40:51] This is snippy 4.6.0
Show full stderr[07:40:51] This is snippy 4.6.0 [07:40:51] Written by Torsten Seemann [07:40:51] Obtained from https://github.com/tseemann/snippy [07:40:51] Detected operating system: linux [07:40:51] Enabling bundled linux tools. [07:40:51] Found bwa - /usr/local/bin/bwa [07:40:51] Found bcftools - /usr/local/bin/bcftools [07:40:51] Found samtools - /usr/local/bin/samtools [07:40:51] Found java - /usr/local/bin/java [07:40:51] Found snpEff - /usr/local/bin/snpEff [07:40:51] Found samclip - /usr/local/bin/samclip [07:40:51] Found seqtk - /usr/local/bin/seqtk [07:40:51] Found parallel - /usr/local/bin/parallel [07:40:51] Found freebayes - /usr/local/bin/freebayes [07:40:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:40:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:40:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:40:51] Found vcfuniq - /usr/local/bin/vcfuniq [07:40:51] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:40:51] Found gzip - /bin/gzip [07:40:51] Found vt - /usr/local/bin/vt [07:40:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:40:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:40:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:40:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:40:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:40:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:40:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:40:51] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:41:19] This is snippy 4.6.0
Show full stderr[07:41:19] This is snippy 4.6.0 [07:41:19] Written by Torsten Seemann [07:41:19] Obtained from https://github.com/tseemann/snippy [07:41:19] Detected operating system: linux [07:41:19] Enabling bundled linux tools. [07:41:19] Found bwa - /usr/local/bin/bwa [07:41:19] Found bcftools - /usr/local/bin/bcftools [07:41:19] Found samtools - /usr/local/bin/samtools [07:41:19] Found java - /usr/local/bin/java [07:41:19] Found snpEff - /usr/local/bin/snpEff [07:41:19] Found samclip - /usr/local/bin/samclip [07:41:19] Found seqtk - /usr/local/bin/seqtk [07:41:19] Found parallel - /usr/local/bin/parallel [07:41:19] Found freebayes - /usr/local/bin/freebayes [07:41:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:41:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:41:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:41:19] Found vcfuniq - /usr/local/bin/vcfuniq [07:41:19] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:41:19] Found gzip - /bin/gzip [07:41:19] Found vt - /usr/local/bin/vt [07:41:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:41:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:41:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:41:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:41:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:41:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:41:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:41:20] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:41:28] This is snippy 4.6.0
Show full stderr[07:41:28] This is snippy 4.6.0 [07:41:28] Written by Torsten Seemann [07:41:28] Obtained from https://github.com/tseemann/snippy [07:41:28] Detected operating system: linux [07:41:28] Enabling bundled linux tools. [07:41:28] Found bwa - /usr/local/bin/bwa [07:41:28] Found bcftools - /usr/local/bin/bcftools [07:41:28] Found samtools - /usr/local/bin/samtools [07:41:28] Found java - /usr/local/bin/java [07:41:28] Found snpEff - /usr/local/bin/snpEff [07:41:28] Found samclip - /usr/local/bin/samclip [07:41:28] Found seqtk - /usr/local/bin/seqtk [07:41:28] Found parallel - /usr/local/bin/parallel [07:41:28] Found freebayes - /usr/local/bin/freebayes [07:41:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:41:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:41:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:41:28] Found vcfuniq - /usr/local/bin/vcfuniq [07:41:28] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:41:28] Found gzip - /bin/gzip [07:41:28] Found vt - /usr/local/bin/vt [07:41:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:41:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:41:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:41:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:41:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:41:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:41:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:41:28] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:40:04] This is snippy 4.6.0
Show full stderr[07:40:04] This is snippy 4.6.0 [07:40:04] Written by Torsten Seemann [07:40:04] Obtained from https://github.com/tseemann/snippy [07:40:04] Detected operating system: linux [07:40:04] Enabling bundled linux tools. [07:40:04] Found bwa - /usr/local/bin/bwa [07:40:04] Found bcftools - /usr/local/bin/bcftools [07:40:04] Found samtools - /usr/local/bin/samtools [07:40:04] Found java - /usr/local/bin/java [07:40:04] Found snpEff - /usr/local/bin/snpEff [07:40:04] Found samclip - /usr/local/bin/samclip [07:40:04] Found seqtk - /usr/local/bin/seqtk [07:40:04] Found parallel - /usr/local/bin/parallel [07:40:04] Found freebayes - /usr/local/bin/freebayes [07:40:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:40:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:40:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:40:04] Found vcfuniq - /usr/local/bin/vcfuniq [07:40:04] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:40:04] Found gzip - /bin/gzip [07:40:04] Found vt - /usr/local/bin/vt [07:40:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:40:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:40:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:40:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:40:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:40:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:40:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:40:05] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:41:49] This is snippy 4.6.0
Show full stderr[07:41:49] This is snippy 4.6.0 [07:41:49] Written by Torsten Seemann [07:41:49] Obtained from https://github.com/tseemann/snippy [07:41:49] Detected operating system: linux [07:41:49] Enabling bundled linux tools. [07:41:49] Found bwa - /usr/local/bin/bwa [07:41:49] Found bcftools - /usr/local/bin/bcftools [07:41:49] Found samtools - /usr/local/bin/samtools [07:41:49] Found java - /usr/local/bin/java [07:41:49] Found snpEff - /usr/local/bin/snpEff [07:41:49] Found samclip - /usr/local/bin/samclip [07:41:49] Found seqtk - /usr/local/bin/seqtk [07:41:49] Found parallel - /usr/local/bin/parallel [07:41:49] Found freebayes - /usr/local/bin/freebayes [07:41:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:41:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:41:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:41:49] Found vcfuniq - /usr/local/bin/vcfuniq [07:41:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:41:49] Found gzip - /bin/gzip [07:41:49] Found vt - /usr/local/bin/vt [07:41:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:41:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:41:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:41:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:41:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:41:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:41:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:41:50] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:38:39] This is snippy 4.6.0
Show full stderr[07:38:39] This is snippy 4.6.0 [07:38:39] Written by Torsten Seemann [07:38:39] Obtained from https://github.com/tseemann/snippy [07:38:39] Detected operating system: linux [07:38:39] Enabling bundled linux tools. [07:38:39] Found bwa - /usr/local/bin/bwa [07:38:39] Found bcftools - /usr/local/bin/bcftools [07:38:39] Found samtools - /usr/local/bin/samtools [07:38:39] Found java - /usr/local/bin/java [07:38:39] Found snpEff - /usr/local/bin/snpEff [07:38:39] Found samclip - /usr/local/bin/samclip [07:38:39] Found seqtk - /usr/local/bin/seqtk [07:38:39] Found parallel - /usr/local/bin/parallel [07:38:39] Found freebayes - /usr/local/bin/freebayes [07:38:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:38:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:38:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:38:39] Found vcfuniq - /usr/local/bin/vcfuniq [07:38:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:38:39] Found gzip - /bin/gzip [07:38:39] Found vt - /usr/local/bin/vt [07:38:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:38:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:38:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:38:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:38:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:38:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:38:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:38:40] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:39:06] This is snippy 4.6.0
Show full stderr[07:39:06] This is snippy 4.6.0 [07:39:06] Written by Torsten Seemann [07:39:06] Obtained from https://github.com/tseemann/snippy [07:39:06] Detected operating system: linux [07:39:06] Enabling bundled linux tools. [07:39:06] Found bwa - /usr/local/bin/bwa [07:39:06] Found bcftools - /usr/local/bin/bcftools [07:39:06] Found samtools - /usr/local/bin/samtools [07:39:06] Found java - /usr/local/bin/java [07:39:06] Found snpEff - /usr/local/bin/snpEff [07:39:06] Found samclip - /usr/local/bin/samclip [07:39:06] Found seqtk - /usr/local/bin/seqtk [07:39:06] Found parallel - /usr/local/bin/parallel [07:39:06] Found freebayes - /usr/local/bin/freebayes [07:39:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:39:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:39:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:39:06] Found vcfuniq - /usr/local/bin/vcfuniq [07:39:06] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:39:07] Found gzip - /bin/gzip [07:39:07] Found vt - /usr/local/bin/vt [07:39:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:39:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:39:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:39:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:39:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:39:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:39:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:39:07] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:39:21] This is snippy 4.6.0
Show full stderr[07:39:21] This is snippy 4.6.0 [07:39:21] Written by Torsten Seemann [07:39:21] Obtained from https://github.com/tseemann/snippy [07:39:21] Detected operating system: linux [07:39:21] Enabling bundled linux tools. [07:39:21] Found bwa - /usr/local/bin/bwa [07:39:21] Found bcftools - /usr/local/bin/bcftools [07:39:21] Found samtools - /usr/local/bin/samtools [07:39:21] Found java - /usr/local/bin/java [07:39:21] Found snpEff - /usr/local/bin/snpEff [07:39:21] Found samclip - /usr/local/bin/samclip [07:39:21] Found seqtk - /usr/local/bin/seqtk [07:39:21] Found parallel - /usr/local/bin/parallel [07:39:21] Found freebayes - /usr/local/bin/freebayes [07:39:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:39:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:39:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:39:21] Found vcfuniq - /usr/local/bin/vcfuniq [07:39:21] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:39:22] Found gzip - /bin/gzip [07:39:22] Found vt - /usr/local/bin/vt [07:39:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:39:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:39:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:39:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:39:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:39:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:39:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:39:22] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:39:24] This is snippy 4.6.0
Show full stderr[07:39:24] This is snippy 4.6.0 [07:39:24] Written by Torsten Seemann [07:39:24] Obtained from https://github.com/tseemann/snippy [07:39:24] Detected operating system: linux [07:39:24] Enabling bundled linux tools. [07:39:24] Found bwa - /usr/local/bin/bwa [07:39:24] Found bcftools - /usr/local/bin/bcftools [07:39:24] Found samtools - /usr/local/bin/samtools [07:39:24] Found java - /usr/local/bin/java [07:39:24] Found snpEff - /usr/local/bin/snpEff [07:39:24] Found samclip - /usr/local/bin/samclip [07:39:24] Found seqtk - /usr/local/bin/seqtk [07:39:24] Found parallel - /usr/local/bin/parallel [07:39:24] Found freebayes - /usr/local/bin/freebayes [07:39:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:39:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:39:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:39:24] Found vcfuniq - /usr/local/bin/vcfuniq [07:39:24] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:39:24] Found gzip - /bin/gzip [07:39:24] Found vt - /usr/local/bin/vt [07:39:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:39:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:39:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:39:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:39:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:39:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:39:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:39:25] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:42:02] This is snippy 4.6.0
Show full stderr[07:42:02] This is snippy 4.6.0 [07:42:02] Written by Torsten Seemann [07:42:02] Obtained from https://github.com/tseemann/snippy [07:42:02] Detected operating system: linux [07:42:02] Enabling bundled linux tools. [07:42:02] Found bwa - /usr/local/bin/bwa [07:42:02] Found bcftools - /usr/local/bin/bcftools [07:42:02] Found samtools - /usr/local/bin/samtools [07:42:02] Found java - /usr/local/bin/java [07:42:02] Found snpEff - /usr/local/bin/snpEff [07:42:02] Found samclip - /usr/local/bin/samclip [07:42:02] Found seqtk - /usr/local/bin/seqtk [07:42:02] Found parallel - /usr/local/bin/parallel [07:42:02] Found freebayes - /usr/local/bin/freebayes [07:42:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:42:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:42:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:42:02] Found vcfuniq - /usr/local/bin/vcfuniq [07:42:02] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:42:02] Found gzip - /bin/gzip [07:42:02] Found vt - /usr/local/bin/vt [07:42:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:42:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:42:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:42:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:42:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:42:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:42:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:42:03] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:44:43] This is snippy 4.6.0
Show full stderr[07:44:43] This is snippy 4.6.0 [07:44:43] Written by Torsten Seemann [07:44:43] Obtained from https://github.com/tseemann/snippy [07:44:43] Detected operating system: linux [07:44:43] Enabling bundled linux tools. [07:44:43] Found bwa - /usr/local/bin/bwa [07:44:43] Found bcftools - /usr/local/bin/bcftools [07:44:43] Found samtools - /usr/local/bin/samtools [07:44:43] Found java - /usr/local/bin/java [07:44:43] Found snpEff - /usr/local/bin/snpEff [07:44:43] Found samclip - /usr/local/bin/samclip [07:44:43] Found seqtk - /usr/local/bin/seqtk [07:44:43] Found parallel - /usr/local/bin/parallel [07:44:43] Found freebayes - /usr/local/bin/freebayes [07:44:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:44:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:44:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:44:43] Found vcfuniq - /usr/local/bin/vcfuniq [07:44:43] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:44:43] Found gzip - /bin/gzip [07:44:43] Found vt - /usr/local/bin/vt [07:44:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:44:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:44:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:44:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:44:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:44:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:44:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:44:44] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:46:16] This is snippy 4.6.0
Show full stderr[07:46:16] This is snippy 4.6.0 [07:46:16] Written by Torsten Seemann [07:46:16] Obtained from https://github.com/tseemann/snippy [07:46:16] Detected operating system: linux [07:46:16] Enabling bundled linux tools. [07:46:16] Found bwa - /usr/local/bin/bwa [07:46:16] Found bcftools - /usr/local/bin/bcftools [07:46:16] Found samtools - /usr/local/bin/samtools [07:46:16] Found java - /usr/local/bin/java [07:46:16] Found snpEff - /usr/local/bin/snpEff [07:46:16] Found samclip - /usr/local/bin/samclip [07:46:16] Found seqtk - /usr/local/bin/seqtk [07:46:16] Found parallel - /usr/local/bin/parallel [07:46:16] Found freebayes - /usr/local/bin/freebayes [07:46:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:46:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:46:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:46:16] Found vcfuniq - /usr/local/bin/vcfuniq [07:46:16] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:46:16] Found gzip - /bin/gzip [07:46:16] Found vt - /usr/local/bin/vt [07:46:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:46:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:46:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:46:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:46:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:46:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:46:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:46:17] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:46:43] This is snippy 4.6.0
Show full stderr[07:46:43] This is snippy 4.6.0 [07:46:43] Written by Torsten Seemann [07:46:43] Obtained from https://github.com/tseemann/snippy [07:46:43] Detected operating system: linux [07:46:43] Enabling bundled linux tools. [07:46:43] Found bwa - /usr/local/bin/bwa [07:46:43] Found bcftools - /usr/local/bin/bcftools [07:46:43] Found samtools - /usr/local/bin/samtools [07:46:43] Found java - /usr/local/bin/java [07:46:43] Found snpEff - /usr/local/bin/snpEff [07:46:43] Found samclip - /usr/local/bin/samclip [07:46:43] Found seqtk - /usr/local/bin/seqtk [07:46:43] Found parallel - /usr/local/bin/parallel [07:46:43] Found freebayes - /usr/local/bin/freebayes [07:46:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:46:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:46:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:46:43] Found vcfuniq - /usr/local/bin/vcfuniq [07:46:43] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:46:43] Found gzip - /bin/gzip [07:46:43] Found vt - /usr/local/bin/vt [07:46:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:46:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:46:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:46:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:46:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:46:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:46:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:46:44] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:46:58] This is snippy 4.6.0
Show full stderr[07:46:58] This is snippy 4.6.0 [07:46:58] Written by Torsten Seemann [07:46:58] Obtained from https://github.com/tseemann/snippy [07:46:58] Detected operating system: linux [07:46:58] Enabling bundled linux tools. [07:46:58] Found bwa - /usr/local/bin/bwa [07:46:58] Found bcftools - /usr/local/bin/bcftools [07:46:58] Found samtools - /usr/local/bin/samtools [07:46:58] Found java - /usr/local/bin/java [07:46:58] Found snpEff - /usr/local/bin/snpEff [07:46:58] Found samclip - /usr/local/bin/samclip [07:46:58] Found seqtk - /usr/local/bin/seqtk [07:46:58] Found parallel - /usr/local/bin/parallel [07:46:58] Found freebayes - /usr/local/bin/freebayes [07:46:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:46:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:46:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:46:58] Found vcfuniq - /usr/local/bin/vcfuniq [07:46:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:46:58] Found gzip - /bin/gzip [07:46:58] Found vt - /usr/local/bin/vt [07:46:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:46:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:46:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:46:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:46:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:46:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:46:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:46:59] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:43:22] This is snippy 4.6.0
Show full stderr[07:43:22] This is snippy 4.6.0 [07:43:22] Written by Torsten Seemann [07:43:22] Obtained from https://github.com/tseemann/snippy [07:43:22] Detected operating system: linux [07:43:22] Enabling bundled linux tools. [07:43:22] Found bwa - /usr/local/bin/bwa [07:43:22] Found bcftools - /usr/local/bin/bcftools [07:43:22] Found samtools - /usr/local/bin/samtools [07:43:22] Found java - /usr/local/bin/java [07:43:22] Found snpEff - /usr/local/bin/snpEff [07:43:22] Found samclip - /usr/local/bin/samclip [07:43:22] Found seqtk - /usr/local/bin/seqtk [07:43:22] Found parallel - /usr/local/bin/parallel [07:43:22] Found freebayes - /usr/local/bin/freebayes [07:43:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:43:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:43:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:43:22] Found vcfuniq - /usr/local/bin/vcfuniq [07:43:22] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:43:22] Found gzip - /bin/gzip [07:43:22] Found vt - /usr/local/bin/vt [07:43:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:43:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:43:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:43:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:43:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:43:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:43:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:43:23] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:46:31] This is snippy 4.6.0
Show full stderr[07:46:31] This is snippy 4.6.0 [07:46:31] Written by Torsten Seemann [07:46:31] Obtained from https://github.com/tseemann/snippy [07:46:31] Detected operating system: linux [07:46:31] Enabling bundled linux tools. [07:46:31] Found bwa - /usr/local/bin/bwa [07:46:31] Found bcftools - /usr/local/bin/bcftools [07:46:31] Found samtools - /usr/local/bin/samtools [07:46:31] Found java - /usr/local/bin/java [07:46:31] Found snpEff - /usr/local/bin/snpEff [07:46:31] Found samclip - /usr/local/bin/samclip [07:46:31] Found seqtk - /usr/local/bin/seqtk [07:46:31] Found parallel - /usr/local/bin/parallel [07:46:31] Found freebayes - /usr/local/bin/freebayes [07:46:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:46:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:46:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:46:31] Found vcfuniq - /usr/local/bin/vcfuniq [07:46:31] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:46:31] Found gzip - /bin/gzip [07:46:31] Found vt - /usr/local/bin/vt [07:46:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:46:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:46:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:46:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:46:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:46:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:46:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:46:32] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:39:36] This is snippy 4.6.0
Show full stderr[07:39:36] This is snippy 4.6.0 [07:39:36] Written by Torsten Seemann [07:39:36] Obtained from https://github.com/tseemann/snippy [07:39:36] Detected operating system: linux [07:39:36] Enabling bundled linux tools. [07:39:36] Found bwa - /usr/local/bin/bwa [07:39:36] Found bcftools - /usr/local/bin/bcftools [07:39:36] Found samtools - /usr/local/bin/samtools [07:39:36] Found java - /usr/local/bin/java [07:39:36] Found snpEff - /usr/local/bin/snpEff [07:39:36] Found samclip - /usr/local/bin/samclip [07:39:36] Found seqtk - /usr/local/bin/seqtk [07:39:36] Found parallel - /usr/local/bin/parallel [07:39:36] Found freebayes - /usr/local/bin/freebayes [07:39:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:39:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:39:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:39:36] Found vcfuniq - /usr/local/bin/vcfuniq [07:39:36] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:39:36] Found gzip - /bin/gzip [07:39:36] Found vt - /usr/local/bin/vt [07:39:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:39:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:39:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:39:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:39:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:39:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:39:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:39:37] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:41:34] This is snippy 4.6.0
Show full stderr[07:41:34] This is snippy 4.6.0 [07:41:34] Written by Torsten Seemann [07:41:34] Obtained from https://github.com/tseemann/snippy [07:41:34] Detected operating system: linux [07:41:34] Enabling bundled linux tools. [07:41:34] Found bwa - /usr/local/bin/bwa [07:41:34] Found bcftools - /usr/local/bin/bcftools [07:41:34] Found samtools - /usr/local/bin/samtools [07:41:34] Found java - /usr/local/bin/java [07:41:34] Found snpEff - /usr/local/bin/snpEff [07:41:34] Found samclip - /usr/local/bin/samclip [07:41:34] Found seqtk - /usr/local/bin/seqtk [07:41:34] Found parallel - /usr/local/bin/parallel [07:41:34] Found freebayes - /usr/local/bin/freebayes [07:41:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:41:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:41:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:41:34] Found vcfuniq - /usr/local/bin/vcfuniq [07:41:34] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:41:34] Found gzip - /bin/gzip [07:41:34] Found vt - /usr/local/bin/vt [07:41:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:41:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:41:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:41:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:41:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:41:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:41:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:41:34] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:41:56] This is snippy 4.6.0
Show full stderr[07:41:56] This is snippy 4.6.0 [07:41:56] Written by Torsten Seemann [07:41:56] Obtained from https://github.com/tseemann/snippy [07:41:56] Detected operating system: linux [07:41:56] Enabling bundled linux tools. [07:41:56] Found bwa - /usr/local/bin/bwa [07:41:56] Found bcftools - /usr/local/bin/bcftools [07:41:56] Found samtools - /usr/local/bin/samtools [07:41:56] Found java - /usr/local/bin/java [07:41:56] Found snpEff - /usr/local/bin/snpEff [07:41:56] Found samclip - /usr/local/bin/samclip [07:41:56] Found seqtk - /usr/local/bin/seqtk [07:41:56] Found parallel - /usr/local/bin/parallel [07:41:56] Found freebayes - /usr/local/bin/freebayes [07:41:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:41:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:41:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:41:56] Found vcfuniq - /usr/local/bin/vcfuniq [07:41:56] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:41:56] Found gzip - /bin/gzip [07:41:56] Found vt - /usr/local/bin/vt [07:41:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:41:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:41:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:41:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:41:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:41:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:41:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:41:57] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:42:16] This is snippy 4.6.0
Show full stderr[07:42:16] This is snippy 4.6.0 [07:42:16] Written by Torsten Seemann [07:42:16] Obtained from https://github.com/tseemann/snippy [07:42:16] Detected operating system: linux [07:42:16] Enabling bundled linux tools. [07:42:16] Found bwa - /usr/local/bin/bwa [07:42:16] Found bcftools - /usr/local/bin/bcftools [07:42:16] Found samtools - /usr/local/bin/samtools [07:42:16] Found java - /usr/local/bin/java [07:42:16] Found snpEff - /usr/local/bin/snpEff [07:42:16] Found samclip - /usr/local/bin/samclip [07:42:16] Found seqtk - /usr/local/bin/seqtk [07:42:16] Found parallel - /usr/local/bin/parallel [07:42:16] Found freebayes - /usr/local/bin/freebayes [07:42:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:42:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:42:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:42:16] Found vcfuniq - /usr/local/bin/vcfuniq [07:42:16] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:42:16] Found gzip - /bin/gzip [07:42:16] Found vt - /usr/local/bin/vt [07:42:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:42:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:42:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:42:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:42:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:42:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:42:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:42:17] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:47:41] This is snippy 4.6.0
Show full stderr[07:47:41] This is snippy 4.6.0 [07:47:41] Written by Torsten Seemann [07:47:41] Obtained from https://github.com/tseemann/snippy [07:47:41] Detected operating system: linux [07:47:41] Enabling bundled linux tools. [07:47:41] Found bwa - /usr/local/bin/bwa [07:47:41] Found bcftools - /usr/local/bin/bcftools [07:47:41] Found samtools - /usr/local/bin/samtools [07:47:41] Found java - /usr/local/bin/java [07:47:41] Found snpEff - /usr/local/bin/snpEff [07:47:41] Found samclip - /usr/local/bin/samclip [07:47:41] Found seqtk - /usr/local/bin/seqtk [07:47:41] Found parallel - /usr/local/bin/parallel [07:47:41] Found freebayes - /usr/local/bin/freebayes [07:47:41] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:47:41] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:47:41] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:47:41] Found vcfuniq - /usr/local/bin/vcfuniq [07:47:41] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:47:41] Found gzip - /bin/gzip [07:47:41] Found vt - /usr/local/bin/vt [07:47:41] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:47:41] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:47:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:47:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:47:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:47:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:47:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:47:42] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:47:53] This is snippy 4.6.0
Show full stderr[07:47:53] This is snippy 4.6.0 [07:47:53] Written by Torsten Seemann [07:47:53] Obtained from https://github.com/tseemann/snippy [07:47:53] Detected operating system: linux [07:47:53] Enabling bundled linux tools. [07:47:53] Found bwa - /usr/local/bin/bwa [07:47:53] Found bcftools - /usr/local/bin/bcftools [07:47:53] Found samtools - /usr/local/bin/samtools [07:47:53] Found java - /usr/local/bin/java [07:47:53] Found snpEff - /usr/local/bin/snpEff [07:47:53] Found samclip - /usr/local/bin/samclip [07:47:53] Found seqtk - /usr/local/bin/seqtk [07:47:53] Found parallel - /usr/local/bin/parallel [07:47:53] Found freebayes - /usr/local/bin/freebayes [07:47:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:47:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:47:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:47:53] Found vcfuniq - /usr/local/bin/vcfuniq [07:47:53] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:47:53] Found gzip - /bin/gzip [07:47:53] Found vt - /usr/local/bin/vt [07:47:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:47:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:47:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:47:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:47:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:47:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:47:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:47:54] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:48:07] This is snippy 4.6.0
Show full stderr[07:48:07] This is snippy 4.6.0 [07:48:07] Written by Torsten Seemann [07:48:07] Obtained from https://github.com/tseemann/snippy [07:48:07] Detected operating system: linux [07:48:07] Enabling bundled linux tools. [07:48:07] Found bwa - /usr/local/bin/bwa [07:48:07] Found bcftools - /usr/local/bin/bcftools [07:48:07] Found samtools - /usr/local/bin/samtools [07:48:07] Found java - /usr/local/bin/java [07:48:07] Found snpEff - /usr/local/bin/snpEff [07:48:07] Found samclip - /usr/local/bin/samclip [07:48:07] Found seqtk - /usr/local/bin/seqtk [07:48:07] Found parallel - /usr/local/bin/parallel [07:48:07] Found freebayes - /usr/local/bin/freebayes [07:48:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:48:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:48:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:48:07] Found vcfuniq - /usr/local/bin/vcfuniq [07:48:07] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:48:07] Found gzip - /bin/gzip [07:48:07] Found vt - /usr/local/bin/vt [07:48:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:48:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:48:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:48:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:48:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:48:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:48:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:48:08] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:48:47] This is snippy 4.6.0
Show full stderr[07:48:47] This is snippy 4.6.0 [07:48:47] Written by Torsten Seemann [07:48:47] Obtained from https://github.com/tseemann/snippy [07:48:47] Detected operating system: linux [07:48:47] Enabling bundled linux tools. [07:48:47] Found bwa - /usr/local/bin/bwa [07:48:47] Found bcftools - /usr/local/bin/bcftools [07:48:47] Found samtools - /usr/local/bin/samtools [07:48:47] Found java - /usr/local/bin/java [07:48:47] Found snpEff - /usr/local/bin/snpEff [07:48:47] Found samclip - /usr/local/bin/samclip [07:48:47] Found seqtk - /usr/local/bin/seqtk [07:48:47] Found parallel - /usr/local/bin/parallel [07:48:47] Found freebayes - /usr/local/bin/freebayes [07:48:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:48:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:48:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:48:47] Found vcfuniq - /usr/local/bin/vcfuniq [07:48:47] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:48:47] Found gzip - /bin/gzip [07:48:47] Found vt - /usr/local/bin/vt [07:48:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:48:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:48:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:48:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:48:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:48:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:48:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:48:48] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:43:10] This is snippy 4.6.0
Show full stderr[07:43:10] This is snippy 4.6.0 [07:43:10] Written by Torsten Seemann [07:43:10] Obtained from https://github.com/tseemann/snippy [07:43:10] Detected operating system: linux [07:43:10] Enabling bundled linux tools. [07:43:10] Found bwa - /usr/local/bin/bwa [07:43:10] Found bcftools - /usr/local/bin/bcftools [07:43:10] Found samtools - /usr/local/bin/samtools [07:43:10] Found java - /usr/local/bin/java [07:43:10] Found snpEff - /usr/local/bin/snpEff [07:43:10] Found samclip - /usr/local/bin/samclip [07:43:10] Found seqtk - /usr/local/bin/seqtk [07:43:10] Found parallel - /usr/local/bin/parallel [07:43:10] Found freebayes - /usr/local/bin/freebayes [07:43:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:43:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:43:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:43:10] Found vcfuniq - /usr/local/bin/vcfuniq [07:43:10] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:43:10] Found gzip - /bin/gzip [07:43:10] Found vt - /usr/local/bin/vt [07:43:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:43:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:43:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:43:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:43:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:43:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:43:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:43:11] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:43:48] This is snippy 4.6.0
Show full stderr[07:43:48] This is snippy 4.6.0 [07:43:48] Written by Torsten Seemann [07:43:48] Obtained from https://github.com/tseemann/snippy [07:43:48] Detected operating system: linux [07:43:48] Enabling bundled linux tools. [07:43:48] Found bwa - /usr/local/bin/bwa [07:43:48] Found bcftools - /usr/local/bin/bcftools [07:43:48] Found samtools - /usr/local/bin/samtools [07:43:48] Found java - /usr/local/bin/java [07:43:48] Found snpEff - /usr/local/bin/snpEff [07:43:48] Found samclip - /usr/local/bin/samclip [07:43:48] Found seqtk - /usr/local/bin/seqtk [07:43:48] Found parallel - /usr/local/bin/parallel [07:43:48] Found freebayes - /usr/local/bin/freebayes [07:43:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:43:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:43:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:43:48] Found vcfuniq - /usr/local/bin/vcfuniq [07:43:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:43:48] Found gzip - /bin/gzip [07:43:48] Found vt - /usr/local/bin/vt [07:43:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:43:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:43:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:43:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:43:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:43:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:43:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:43:49] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:44:28] This is snippy 4.6.0
Show full stderr[07:44:28] This is snippy 4.6.0 [07:44:28] Written by Torsten Seemann [07:44:28] Obtained from https://github.com/tseemann/snippy [07:44:28] Detected operating system: linux [07:44:28] Enabling bundled linux tools. [07:44:28] Found bwa - /usr/local/bin/bwa [07:44:28] Found bcftools - /usr/local/bin/bcftools [07:44:28] Found samtools - /usr/local/bin/samtools [07:44:28] Found java - /usr/local/bin/java [07:44:28] Found snpEff - /usr/local/bin/snpEff [07:44:28] Found samclip - /usr/local/bin/samclip [07:44:28] Found seqtk - /usr/local/bin/seqtk [07:44:28] Found parallel - /usr/local/bin/parallel [07:44:28] Found freebayes - /usr/local/bin/freebayes [07:44:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:44:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:44:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:44:28] Found vcfuniq - /usr/local/bin/vcfuniq [07:44:28] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:44:28] Found gzip - /bin/gzip [07:44:28] Found vt - /usr/local/bin/vt [07:44:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:44:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:44:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:44:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:44:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:44:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:44:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:44:29] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:42:40] This is snippy 4.6.0
Show full stderr[07:42:40] This is snippy 4.6.0 [07:42:40] Written by Torsten Seemann [07:42:40] Obtained from https://github.com/tseemann/snippy [07:42:40] Detected operating system: linux [07:42:40] Enabling bundled linux tools. [07:42:40] Found bwa - /usr/local/bin/bwa [07:42:40] Found bcftools - /usr/local/bin/bcftools [07:42:40] Found samtools - /usr/local/bin/samtools [07:42:40] Found java - /usr/local/bin/java [07:42:40] Found snpEff - /usr/local/bin/snpEff [07:42:40] Found samclip - /usr/local/bin/samclip [07:42:40] Found seqtk - /usr/local/bin/seqtk [07:42:40] Found parallel - /usr/local/bin/parallel [07:42:40] Found freebayes - /usr/local/bin/freebayes [07:42:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:42:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:42:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:42:40] Found vcfuniq - /usr/local/bin/vcfuniq [07:42:40] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:42:40] Found gzip - /bin/gzip [07:42:40] Found vt - /usr/local/bin/vt [07:42:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:42:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:42:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:42:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:42:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:42:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:42:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:42:41] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:42:55] This is snippy 4.6.0
Show full stderr[07:42:55] This is snippy 4.6.0 [07:42:55] Written by Torsten Seemann [07:42:55] Obtained from https://github.com/tseemann/snippy [07:42:55] Detected operating system: linux [07:42:55] Enabling bundled linux tools. [07:42:55] Found bwa - /usr/local/bin/bwa [07:42:55] Found bcftools - /usr/local/bin/bcftools [07:42:55] Found samtools - /usr/local/bin/samtools [07:42:55] Found java - /usr/local/bin/java [07:42:55] Found snpEff - /usr/local/bin/snpEff [07:42:55] Found samclip - /usr/local/bin/samclip [07:42:55] Found seqtk - /usr/local/bin/seqtk [07:42:55] Found parallel - /usr/local/bin/parallel [07:42:55] Found freebayes - /usr/local/bin/freebayes [07:42:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:42:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:42:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:42:55] Found vcfuniq - /usr/local/bin/vcfuniq [07:42:55] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:42:55] Found gzip - /bin/gzip [07:42:55] Found vt - /usr/local/bin/vt [07:42:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:42:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:42:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:42:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:42:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:42:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:42:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:42:56] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:49:02] This is snippy 4.6.0
Show full stderr[07:49:02] This is snippy 4.6.0 [07:49:02] Written by Torsten Seemann [07:49:02] Obtained from https://github.com/tseemann/snippy [07:49:02] Detected operating system: linux [07:49:02] Enabling bundled linux tools. [07:49:02] Found bwa - /usr/local/bin/bwa [07:49:02] Found bcftools - /usr/local/bin/bcftools [07:49:02] Found samtools - /usr/local/bin/samtools [07:49:02] Found java - /usr/local/bin/java [07:49:02] Found snpEff - /usr/local/bin/snpEff [07:49:02] Found samclip - /usr/local/bin/samclip [07:49:02] Found seqtk - /usr/local/bin/seqtk [07:49:02] Found parallel - /usr/local/bin/parallel [07:49:02] Found freebayes - /usr/local/bin/freebayes [07:49:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:49:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:49:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:49:02] Found vcfuniq - /usr/local/bin/vcfuniq [07:49:02] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:49:02] Found gzip - /bin/gzip [07:49:02] Found vt - /usr/local/bin/vt [07:49:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:49:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:49:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:49:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:49:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:49:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:49:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:49:03] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:49:19] This is snippy 4.6.0
Show full stderr[07:49:19] This is snippy 4.6.0 [07:49:19] Written by Torsten Seemann [07:49:19] Obtained from https://github.com/tseemann/snippy [07:49:19] Detected operating system: linux [07:49:19] Enabling bundled linux tools. [07:49:19] Found bwa - /usr/local/bin/bwa [07:49:19] Found bcftools - /usr/local/bin/bcftools [07:49:19] Found samtools - /usr/local/bin/samtools [07:49:19] Found java - /usr/local/bin/java [07:49:19] Found snpEff - /usr/local/bin/snpEff [07:49:19] Found samclip - /usr/local/bin/samclip [07:49:19] Found seqtk - /usr/local/bin/seqtk [07:49:19] Found parallel - /usr/local/bin/parallel [07:49:19] Found freebayes - /usr/local/bin/freebayes [07:49:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:49:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:49:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:49:19] Found vcfuniq - /usr/local/bin/vcfuniq [07:49:19] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:49:19] Found gzip - /bin/gzip [07:49:19] Found vt - /usr/local/bin/vt [07:49:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:49:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:49:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:49:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:49:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:49:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:49:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:49:20] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:49:34] This is snippy 4.6.0
Show full stderr[07:49:34] This is snippy 4.6.0 [07:49:34] Written by Torsten Seemann [07:49:34] Obtained from https://github.com/tseemann/snippy [07:49:34] Detected operating system: linux [07:49:34] Enabling bundled linux tools. [07:49:34] Found bwa - /usr/local/bin/bwa [07:49:34] Found bcftools - /usr/local/bin/bcftools [07:49:34] Found samtools - /usr/local/bin/samtools [07:49:34] Found java - /usr/local/bin/java [07:49:34] Found snpEff - /usr/local/bin/snpEff [07:49:34] Found samclip - /usr/local/bin/samclip [07:49:34] Found seqtk - /usr/local/bin/seqtk [07:49:34] Found parallel - /usr/local/bin/parallel [07:49:34] Found freebayes - /usr/local/bin/freebayes [07:49:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:49:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:49:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:49:34] Found vcfuniq - /usr/local/bin/vcfuniq [07:49:34] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:49:34] Found gzip - /bin/gzip [07:49:34] Found vt - /usr/local/bin/vt [07:49:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:49:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:49:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:49:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:49:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:49:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:49:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:49:35] Please supply a reference FASTA/GBK/EMBL file with --reference
2[07:46:01] This is snippy 4.6.0
Show full stderr[07:46:01] This is snippy 4.6.0 [07:46:01] Written by Torsten Seemann [07:46:01] Obtained from https://github.com/tseemann/snippy [07:46:01] Detected operating system: linux [07:46:01] Enabling bundled linux tools. [07:46:01] Found bwa - /usr/local/bin/bwa [07:46:01] Found bcftools - /usr/local/bin/bcftools [07:46:01] Found samtools - /usr/local/bin/samtools [07:46:01] Found java - /usr/local/bin/java [07:46:01] Found snpEff - /usr/local/bin/snpEff [07:46:01] Found samclip - /usr/local/bin/samclip [07:46:01] Found seqtk - /usr/local/bin/seqtk [07:46:01] Found parallel - /usr/local/bin/parallel [07:46:01] Found freebayes - /usr/local/bin/freebayes [07:46:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:46:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:46:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:46:01] Found vcfuniq - /usr/local/bin/vcfuniq [07:46:01] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:46:01] Found gzip - /bin/gzip [07:46:01] Found vt - /usr/local/bin/vt [07:46:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:46:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:46:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:46:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:46:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:46:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:46:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:46:02] Please supply a reference FASTA/GBK/EMBL file with --reference
2[09:18:44] This is snippy 4.6.0
Show full stderr[09:18:44] This is snippy 4.6.0 [09:18:44] Written by Torsten Seemann [09:18:44] Obtained from https://github.com/tseemann/snippy [09:18:44] Detected operating system: linux [09:18:44] Enabling bundled linux tools. [09:18:44] Found bwa - /usr/local/bin/bwa [09:18:44] Found bcftools - /usr/local/bin/bcftools [09:18:44] Found samtools - /usr/local/bin/samtools [09:18:44] Found java - /usr/local/bin/java [09:18:44] Found snpEff - /usr/local/bin/snpEff [09:18:44] Found samclip - /usr/local/bin/samclip [09:18:44] Found seqtk - /usr/local/bin/seqtk [09:18:44] Found parallel - /usr/local/bin/parallel [09:18:44] Found freebayes - /usr/local/bin/freebayes [09:18:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [09:18:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [09:18:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [09:18:45] Found vcfuniq - /usr/local/bin/vcfuniq [09:18:45] Found vcffirstheader - /usr/local/bin/vcffirstheader [09:18:45] Found gzip - /bin/gzip [09:18:45] Found vt - /usr/local/bin/vt [09:18:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [09:18:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [09:18:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [09:18:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [09:18:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [09:18:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [09:18:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [09:18:45] Using reference: /cvmfs/data.galaxyproject.org/byhand/Araly1/seq/Araly1.fa [09:18:51] Treating reference as 'fasta' format. [09:18:51] Will use 1 CPU cores. [09:18:51] Using read file: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat [09:18:51] Using read file: /corral4/main/objects/e/5/6/dataset_e56285d3-c227-475c-8ad7-daa6925b1921.dat [09:18:51] Creating folder: GCF_000195955_2_ASM19595v2_genomic_fna [09:18:51] Changing working directory: GCF_000195955_2_ASM19595v2_genomic_fna [09:18:51] Creating reference folder: reference [09:18:51] Extracting FASTA and GFF from reference. [09:18:59] Wrote 702 sequences to ref.fa [09:18:59] Wrote 0 features to ref.gff [09:18:59] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time. [09:18:59] Using BAM RG (Read Group) ID: GCF_000195955_2_ASM19595v2_genomic_fna [09:18:59] Running: samtools faidx reference/ref.fa 2>> snps.log [09:18:59] Error running command, check GCF_000195955_2_ASM19595v2_genomic_fna/snps.log
2[09:20:50] This is snippy 4.6.0
Show full stderr[09:20:50] This is snippy 4.6.0 [09:20:50] Written by Torsten Seemann [09:20:50] Obtained from https://github.com/tseemann/snippy [09:20:50] Detected operating system: linux [09:20:50] Enabling bundled linux tools. [09:20:50] Found bwa - /usr/local/bin/bwa [09:20:50] Found bcftools - /usr/local/bin/bcftools [09:20:50] Found samtools - /usr/local/bin/samtools [09:20:50] Found java - /usr/local/bin/java [09:20:50] Found snpEff - /usr/local/bin/snpEff [09:20:50] Found samclip - /usr/local/bin/samclip [09:20:50] Found seqtk - /usr/local/bin/seqtk [09:20:50] Found parallel - /usr/local/bin/parallel [09:20:50] Found freebayes - /usr/local/bin/freebayes [09:20:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [09:20:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [09:20:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [09:20:50] Found vcfuniq - /usr/local/bin/vcfuniq [09:20:50] Found vcffirstheader - /usr/local/bin/vcffirstheader [09:20:50] Found gzip - /bin/gzip [09:20:50] Found vt - /usr/local/bin/vt [09:20:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [09:20:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [09:20:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [09:20:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [09:20:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [09:20:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [09:20:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [09:20:50] Using reference: /cvmfs/data.galaxyproject.org/byhand/Araly1/seq/Araly1.fa [09:20:51] Treating reference as 'fasta' format. [09:20:51] Will use 1 CPU cores. [09:20:51] Using read file: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat [09:20:51] Using read file: /corral4/main/objects/8/9/d/dataset_89d88cd8-c878-453e-bdcb-ac6b4370d21b.dat [09:20:51] Creating folder: GCF_000195955_2_ASM19595v2_genomic_fna [09:20:51] Changing working directory: GCF_000195955_2_ASM19595v2_genomic_fna [09:20:51] Creating reference folder: reference [09:20:51] Extracting FASTA and GFF from reference. [09:20:58] Wrote 702 sequences to ref.fa [09:20:58] Wrote 0 features to ref.gff [09:20:59] Freebayes will process 1 chunks of 210374351 bp, 1 chunks at a time. [09:20:59] Using BAM RG (Read Group) ID: GCF_000195955_2_ASM19595v2_genomic_fna [09:20:59] Running: samtools faidx reference/ref.fa 2>> snps.log [09:20:59] Error running command, check GCF_000195955_2_ASM19595v2_genomic_fna/snps.log
2[09:19:11] This is snippy 4.6.0
Show full stderr[09:19:11] This is snippy 4.6.0 [09:19:11] Written by Torsten Seemann [09:19:11] Obtained from https://github.com/tseemann/snippy [09:19:11] Detected operating system: linux [09:19:11] Enabling bundled linux tools. [09:19:11] Found bwa - /usr/local/bin/bwa [09:19:11] Found bcftools - /usr/local/bin/bcftools [09:19:11] Found samtools - /usr/local/bin/samtools [09:19:11] Found java - /usr/local/bin/java [09:19:11] Found snpEff - /usr/local/bin/snpEff [09:19:11] Found samclip - /usr/local/bin/samclip [09:19:11] Found seqtk - /usr/local/bin/seqtk [09:19:11] Found parallel - /usr/local/bin/parallel [09:19:11] Found freebayes - /usr/local/bin/freebayes [09:19:11] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [09:19:11] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [09:19:11] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [09:19:11] Found vcfuniq - /usr/local/bin/vcfuniq [09:19:11] Found vcffirstheader - /usr/local/bin/vcffirstheader [09:19:11] Found gzip - /bin/gzip [09:19:11] Found vt - /usr/local/bin/vt [09:19:11] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [09:19:11] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [09:19:11] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [09:19:11] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [09:19:11] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [09:19:12] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [09:19:12] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [09:19:12] Using reference: /cvmfs/data.galaxyproject.org/byhand/Araly1/seq/Araly1.fa [09:19:13] Treating reference as 'fasta' format. [09:19:13] Will use 1 CPU cores. [09:19:13] Using read file: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat [09:19:13] Using read file: /corral4/main/objects/2/6/8/dataset_268e6c58-daba-4d88-a64e-3107304c568d.dat [09:19:13] Creating folder: GCF_000195955_2_ASM19595v2_genomic_fna [09:19:13] Changing working directory: GCF_000195955_2_ASM19595v2_genomic_fna [09:19:13] Creating reference folder: reference [09:19:13] Extracting FASTA and GFF from reference. [09:19:20] Wrote 702 sequences to ref.fa [09:19:20] Wrote 0 features to ref.gff [09:19:21] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time. [09:19:21] Using BAM RG (Read Group) ID: GCF_000195955_2_ASM19595v2_genomic_fna [09:19:21] Running: samtools faidx reference/ref.fa 2>> snps.log [09:19:21] Error running command, check GCF_000195955_2_ASM19595v2_genomic_fna/snps.log
2[09:19:10] This is snippy 4.6.0
Show full stderr[09:19:10] This is snippy 4.6.0 [09:19:10] Written by Torsten Seemann [09:19:10] Obtained from https://github.com/tseemann/snippy [09:19:10] Detected operating system: linux [09:19:10] Enabling bundled linux tools. [09:19:10] Found bwa - /usr/local/bin/bwa [09:19:10] Found bcftools - /usr/local/bin/bcftools [09:19:10] Found samtools - /usr/local/bin/samtools [09:19:10] Found java - /usr/local/bin/java [09:19:10] Found snpEff - /usr/local/bin/snpEff [09:19:10] Found samclip - /usr/local/bin/samclip [09:19:10] Found seqtk - /usr/local/bin/seqtk [09:19:10] Found parallel - /usr/local/bin/parallel [09:19:10] Found freebayes - /usr/local/bin/freebayes [09:19:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [09:19:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [09:19:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [09:19:11] Found vcfuniq - /usr/local/bin/vcfuniq [09:19:11] Found vcffirstheader - /usr/local/bin/vcffirstheader [09:19:11] Found gzip - /bin/gzip [09:19:11] Found vt - /usr/local/bin/vt [09:19:11] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [09:19:11] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [09:19:11] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [09:19:11] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [09:19:11] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [09:19:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [09:19:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [09:19:11] Using reference: /cvmfs/data.galaxyproject.org/byhand/Araly1/seq/Araly1.fa [09:19:12] Treating reference as 'fasta' format. [09:19:12] Will use 1 CPU cores. [09:19:12] Using read file: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat [09:19:12] Using read file: /corral4/main/objects/f/d/8/dataset_fd86cbff-ece5-4b83-858e-002d4b59aca9.dat [09:19:12] Creating folder: GCF_000195955_2_ASM19595v2_genomic_fna [09:19:12] Changing working directory: GCF_000195955_2_ASM19595v2_genomic_fna [09:19:12] Creating reference folder: reference [09:19:12] Extracting FASTA and GFF from reference. [09:19:19] Wrote 702 sequences to ref.fa [09:19:19] Wrote 0 features to ref.gff [09:19:19] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time. [09:19:19] Using BAM RG (Read Group) ID: GCF_000195955_2_ASM19595v2_genomic_fna [09:19:20] Running: samtools faidx reference/ref.fa 2>> snps.log [09:19:20] Error running command, check GCF_000195955_2_ASM19595v2_genomic_fna/snps.log
2[09:20:47] This is snippy 4.6.0
Show full stderr[09:20:47] This is snippy 4.6.0 [09:20:47] Written by Torsten Seemann [09:20:47] Obtained from https://github.com/tseemann/snippy [09:20:47] Detected operating system: linux [09:20:47] Enabling bundled linux tools. [09:20:47] Found bwa - /usr/local/bin/bwa [09:20:47] Found bcftools - /usr/local/bin/bcftools [09:20:47] Found samtools - /usr/local/bin/samtools [09:20:47] Found java - /usr/local/bin/java [09:20:47] Found snpEff - /usr/local/bin/snpEff [09:20:47] Found samclip - /usr/local/bin/samclip [09:20:47] Found seqtk - /usr/local/bin/seqtk [09:20:47] Found parallel - /usr/local/bin/parallel [09:20:47] Found freebayes - /usr/local/bin/freebayes [09:20:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [09:20:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [09:20:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [09:20:47] Found vcfuniq - /usr/local/bin/vcfuniq [09:20:47] Found vcffirstheader - /usr/local/bin/vcffirstheader [09:20:47] Found gzip - /bin/gzip [09:20:47] Found vt - /usr/local/bin/vt [09:20:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [09:20:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [09:20:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [09:20:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [09:20:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [09:20:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [09:20:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [09:20:48] Using reference: /cvmfs/data.galaxyproject.org/byhand/Araly1/seq/Araly1.fa [09:20:48] Treating reference as 'fasta' format. [09:20:48] Will use 1 CPU cores. [09:20:48] Using read file: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat [09:20:48] Using read file: /corral4/main/objects/d/0/b/dataset_d0b338bf-adde-498e-a96d-aa7ff4919c6d.dat [09:20:48] Creating folder: GCF_000195955_2_ASM19595v2_genomic_fna [09:20:48] Changing working directory: GCF_000195955_2_ASM19595v2_genomic_fna [09:20:48] Creating reference folder: reference [09:20:48] Extracting FASTA and GFF from reference. [09:20:57] Wrote 702 sequences to ref.fa [09:20:57] Wrote 0 features to ref.gff [09:20:57] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time. [09:20:57] Using BAM RG (Read Group) ID: GCF_000195955_2_ASM19595v2_genomic_fna [09:20:57] Running: samtools faidx reference/ref.fa 2>> snps.log [09:20:57] Error running command, check GCF_000195955_2_ASM19595v2_genomic_fna/snps.log
2[09:22:04] This is snippy 4.6.0
Show full stderr[09:22:04] This is snippy 4.6.0 [09:22:04] Written by Torsten Seemann [09:22:04] Obtained from https://github.com/tseemann/snippy [09:22:04] Detected operating system: linux [09:22:04] Enabling bundled linux tools. [09:22:04] Found bwa - /usr/local/bin/bwa [09:22:04] Found bcftools - /usr/local/bin/bcftools [09:22:04] Found samtools - /usr/local/bin/samtools [09:22:04] Found java - /usr/local/bin/java [09:22:04] Found snpEff - /usr/local/bin/snpEff [09:22:04] Found samclip - /usr/local/bin/samclip [09:22:04] Found seqtk - /usr/local/bin/seqtk [09:22:04] Found parallel - /usr/local/bin/parallel [09:22:04] Found freebayes - /usr/local/bin/freebayes [09:22:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [09:22:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [09:22:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [09:22:04] Found vcfuniq - /usr/local/bin/vcfuniq [09:22:04] Found vcffirstheader - /usr/local/bin/vcffirstheader [09:22:04] Found gzip - /bin/gzip [09:22:04] Found vt - /usr/local/bin/vt [09:22:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [09:22:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [09:22:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [09:22:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [09:22:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [09:22:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [09:22:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [09:22:05] Using reference: /cvmfs/data.galaxyproject.org/byhand/Araly1/seq/Araly1.fa [09:22:06] Treating reference as 'fasta' format. [09:22:06] Will use 1 CPU cores. [09:22:06] Using read file: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat [09:22:06] Using read file: /corral4/main/objects/5/4/d/dataset_54d0ab2a-0024-45c4-9d28-8ab9bed0a92d.dat [09:22:06] Creating folder: GCF_000195955_2_ASM19595v2_genomic_fna [09:22:06] Changing working directory: GCF_000195955_2_ASM19595v2_genomic_fna [09:22:06] Creating reference folder: reference [09:22:06] Extracting FASTA and GFF from reference. [09:22:14] Wrote 702 sequences to ref.fa [09:22:14] Wrote 0 features to ref.gff [09:22:14] Freebayes will process 1 chunks of 210374351 bp, 1 chunks at a time. [09:22:14] Using BAM RG (Read Group) ID: GCF_000195955_2_ASM19595v2_genomic_fna [09:22:14] Running: samtools faidx reference/ref.fa 2>> snps.log [09:22:15] Running: bwa index reference/ref.fa 2>> snps.log [09:27:58] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [09:27:58] Error running command, check GCF_000195955_2_ASM19595v2_genomic_fna/snps.log
2[09:21:41] This is snippy 4.6.0
Show full stderr[09:21:41] This is snippy 4.6.0 [09:21:41] Written by Torsten Seemann [09:21:41] Obtained from https://github.com/tseemann/snippy [09:21:41] Detected operating system: linux [09:21:41] Enabling bundled linux tools. [09:21:41] Found bwa - /usr/local/bin/bwa [09:21:41] Found bcftools - /usr/local/bin/bcftools [09:21:41] Found samtools - /usr/local/bin/samtools [09:21:41] Found java - /usr/local/bin/java [09:21:41] Found snpEff - /usr/local/bin/snpEff [09:21:41] Found samclip - /usr/local/bin/samclip [09:21:41] Found seqtk - /usr/local/bin/seqtk [09:21:41] Found parallel - /usr/local/bin/parallel [09:21:41] Found freebayes - /usr/local/bin/freebayes [09:21:41] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [09:21:41] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [09:21:41] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [09:21:41] Found vcfuniq - /usr/local/bin/vcfuniq [09:21:41] Found vcffirstheader - /usr/local/bin/vcffirstheader [09:21:41] Found gzip - /bin/gzip [09:21:41] Found vt - /usr/local/bin/vt [09:21:41] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [09:21:41] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [09:21:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [09:21:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [09:21:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [09:21:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [09:21:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [09:21:42] Using reference: /cvmfs/data.galaxyproject.org/byhand/Araly1/seq/Araly1.fa [09:21:43] Treating reference as 'fasta' format. [09:21:43] Will use 1 CPU cores. [09:21:43] Using read file: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat [09:21:43] Using read file: /corral4/main/objects/8/1/7/dataset_817afe11-36e0-49b9-9e4f-ff9727bd156d.dat [09:21:43] Creating folder: GCF_000195955_2_ASM19595v2_genomic_fna [09:21:43] Changing working directory: GCF_000195955_2_ASM19595v2_genomic_fna [09:21:43] Creating reference folder: reference [09:21:43] Extracting FASTA and GFF from reference. [09:21:50] Wrote 702 sequences to ref.fa [09:21:50] Wrote 0 features to ref.gff [09:21:51] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time. [09:21:51] Using BAM RG (Read Group) ID: GCF_000195955_2_ASM19595v2_genomic_fna [09:21:51] Running: samtools faidx reference/ref.fa 2>> snps.log [09:21:51] Error running command, check GCF_000195955_2_ASM19595v2_genomic_fna/snps.log
2[13:10:17] This is snippy 4.6.0
Show full stderr[13:10:17] This is snippy 4.6.0 [13:10:17] Written by Torsten Seemann [13:10:17] Obtained from https://github.com/tseemann/snippy [13:10:17] Detected operating system: linux [13:10:17] Enabling bundled linux tools. [13:10:17] Found bwa - /usr/local/bin/bwa [13:10:17] Found bcftools - /usr/local/bin/bcftools [13:10:17] Found samtools - /usr/local/bin/samtools [13:10:17] Found java - /usr/local/bin/java [13:10:17] Found snpEff - /usr/local/bin/snpEff [13:10:18] Found samclip - /usr/local/bin/samclip [13:10:18] Found seqtk - /usr/local/bin/seqtk [13:10:18] Found parallel - /usr/local/bin/parallel [13:10:18] Found freebayes - /usr/local/bin/freebayes [13:10:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [13:10:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [13:10:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [13:10:18] Found vcfuniq - /usr/local/bin/vcfuniq [13:10:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [13:10:18] Found gzip - /bin/gzip [13:10:18] Found vt - /usr/local/bin/vt [13:10:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [13:10:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [13:10:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [13:10:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [13:10:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [13:10:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [13:10:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [13:10:18] Using reference: /jetstream2/scratch/main/jobs/72274633/inputs/dataset_8c4a0e80-4ef9-43df-add5-2cfde861170d.dat [13:10:18] Treating reference as 'fasta' format. [13:10:18] Will use 1 CPU cores. [13:10:18] Using read file: /jetstream2/scratch/main/jobs/72274633/inputs/dataset_937e13a3-f031-450e-ba32-5b187a6037b7.dat [13:10:18] Creating folder: Select_on_dataset_16 [13:10:18] Changing working directory: Select_on_dataset_16 [13:10:18] Creating reference folder: reference [13:10:18] Extracting FASTA and GFF from reference. [13:10:19] Wrote 3 sequences to ref.fa [13:10:19] Wrote 0 features to ref.gff [13:10:19] Freebayes will process 1 chunks of 9205924 bp, 1 chunks at a time. [13:10:19] Using BAM RG (Read Group) ID: Select_on_dataset_16 [13:10:19] Running: samtools faidx reference/ref.fa 2>> snps.log [13:10:19] Running: bwa index reference/ref.fa 2>> snps.log [13:10:21] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [13:10:22] Running: ln -sf reference/ref.fa . 2>> snps.log [13:10:22] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [13:10:22] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [13:10:22] Running: bwa mem -Y -M -R '@RG\tID:Select_on_dataset_16\tSM:Select_on_dataset_16' -t 1 reference/ref.fa /jetstream2/scratch/main/jobs/72274633/inputs/dataset_937e13a3-f031-450e-ba32-5b187a6037b7.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/72274633/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/72274633/tmp --threads 0 -m 12000M | samtools markdup -T /jetstream2/scratch/main/jobs/72274633/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 3 sequences in reference/ref.fa.fai [M::process] read 1 sequences (12466108 bp)... [M::mem_process_seqs] Processed
2[12:50:26] This is snippy 4.6.0
Show full stderr[12:50:26] This is snippy 4.6.0 [12:50:26] Written by Torsten Seemann [12:50:26] Obtained from https://github.com/tseemann/snippy [12:50:26] Detected operating system: linux [12:50:26] Enabling bundled linux tools. [12:50:26] Found bwa - /usr/local/bin/bwa [12:50:26] Found bcftools - /usr/local/bin/bcftools [12:50:26] Found samtools - /usr/local/bin/samtools [12:50:26] Found java - /usr/local/bin/java [12:50:26] Found snpEff - /usr/local/bin/snpEff [12:50:26] Found samclip - /usr/local/bin/samclip [12:50:26] Found seqtk - /usr/local/bin/seqtk [12:50:26] Found parallel - /usr/local/bin/parallel [12:50:26] Found freebayes - /usr/local/bin/freebayes [12:50:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:50:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:50:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:50:26] Found vcfuniq - /usr/local/bin/vcfuniq [12:50:26] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:50:26] Found gzip - /bin/gzip [12:50:26] Found vt - /usr/local/bin/vt [12:50:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:50:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:50:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:50:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:50:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:50:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:50:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:50:27] Please supply a reference FASTA/GBK/EMBL file with --reference
2[12:48:17] This is snippy 4.6.0
Show full stderr[12:48:17] This is snippy 4.6.0 [12:48:17] Written by Torsten Seemann [12:48:17] Obtained from https://github.com/tseemann/snippy [12:48:17] Detected operating system: linux [12:48:17] Enabling bundled linux tools. [12:48:17] Found bwa - /usr/local/bin/bwa [12:48:17] Found bcftools - /usr/local/bin/bcftools [12:48:17] Found samtools - /usr/local/bin/samtools [12:48:17] Found java - /usr/local/bin/java [12:48:17] Found snpEff - /usr/local/bin/snpEff [12:48:17] Found samclip - /usr/local/bin/samclip [12:48:17] Found seqtk - /usr/local/bin/seqtk [12:48:17] Found parallel - /usr/local/bin/parallel [12:48:17] Found freebayes - /usr/local/bin/freebayes [12:48:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:48:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:48:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:48:17] Found vcfuniq - /usr/local/bin/vcfuniq [12:48:17] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:48:17] Found gzip - /bin/gzip [12:48:17] Found vt - /usr/local/bin/vt [12:48:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:48:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:48:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:48:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:48:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:48:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:48:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:48:18] Please supply a reference FASTA/GBK/EMBL file with --reference
2[12:49:55] This is snippy 4.6.0
Show full stderr[12:49:55] This is snippy 4.6.0 [12:49:55] Written by Torsten Seemann [12:49:55] Obtained from https://github.com/tseemann/snippy [12:49:55] Detected operating system: linux [12:49:55] Enabling bundled linux tools. [12:49:55] Found bwa - /usr/local/bin/bwa [12:49:55] Found bcftools - /usr/local/bin/bcftools [12:49:55] Found samtools - /usr/local/bin/samtools [12:49:55] Found java - /usr/local/bin/java [12:49:55] Found snpEff - /usr/local/bin/snpEff [12:49:55] Found samclip - /usr/local/bin/samclip [12:49:55] Found seqtk - /usr/local/bin/seqtk [12:49:55] Found parallel - /usr/local/bin/parallel [12:49:55] Found freebayes - /usr/local/bin/freebayes [12:49:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:49:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:49:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:49:55] Found vcfuniq - /usr/local/bin/vcfuniq [12:49:55] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:49:55] Found gzip - /bin/gzip [12:49:55] Found vt - /usr/local/bin/vt [12:49:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:49:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:49:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:49:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:49:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:49:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:49:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:49:56] Please supply a reference FASTA/GBK/EMBL file with --reference
2[12:52:20] This is snippy 4.6.0
Show full stderr[12:52:20] This is snippy 4.6.0 [12:52:20] Written by Torsten Seemann [12:52:20] Obtained from https://github.com/tseemann/snippy [12:52:20] Detected operating system: linux [12:52:20] Enabling bundled linux tools. [12:52:20] Found bwa - /usr/local/bin/bwa [12:52:20] Found bcftools - /usr/local/bin/bcftools [12:52:20] Found samtools - /usr/local/bin/samtools [12:52:20] Found java - /usr/local/bin/java [12:52:20] Found snpEff - /usr/local/bin/snpEff [12:52:20] Found samclip - /usr/local/bin/samclip [12:52:20] Found seqtk - /usr/local/bin/seqtk [12:52:20] Found parallel - /usr/local/bin/parallel [12:52:20] Found freebayes - /usr/local/bin/freebayes [12:52:20] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:52:20] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:52:20] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:52:20] Found vcfuniq - /usr/local/bin/vcfuniq [12:52:20] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:52:20] Found gzip - /bin/gzip [12:52:20] Found vt - /usr/local/bin/vt [12:52:20] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:52:20] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:52:20] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:52:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:52:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:52:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:52:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:52:21] Please supply a reference FASTA/GBK/EMBL file with --reference
2[12:57:03] This is snippy 4.6.0
Show full stderr[12:57:03] This is snippy 4.6.0 [12:57:03] Written by Torsten Seemann [12:57:03] Obtained from https://github.com/tseemann/snippy [12:57:03] Detected operating system: linux [12:57:03] Enabling bundled linux tools. [12:57:03] Found bwa - /usr/local/bin/bwa [12:57:03] Found bcftools - /usr/local/bin/bcftools [12:57:03] Found samtools - /usr/local/bin/samtools [12:57:03] Found java - /usr/local/bin/java [12:57:03] Found snpEff - /usr/local/bin/snpEff [12:57:03] Found samclip - /usr/local/bin/samclip [12:57:03] Found seqtk - /usr/local/bin/seqtk [12:57:03] Found parallel - /usr/local/bin/parallel [12:57:03] Found freebayes - /usr/local/bin/freebayes [12:57:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:57:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:57:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:57:03] Found vcfuniq - /usr/local/bin/vcfuniq [12:57:03] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:57:03] Found gzip - /bin/gzip [12:57:03] Found vt - /usr/local/bin/vt [12:57:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:57:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:57:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:57:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:57:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:57:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:57:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:57:03] Please supply a reference FASTA/GBK/EMBL file with --reference
2[12:54:13] This is snippy 4.6.0
Show full stderr[12:54:13] This is snippy 4.6.0 [12:54:13] Written by Torsten Seemann [12:54:13] Obtained from https://github.com/tseemann/snippy [12:54:13] Detected operating system: linux [12:54:13] Enabling bundled linux tools. [12:54:13] Found bwa - /usr/local/bin/bwa [12:54:13] Found bcftools - /usr/local/bin/bcftools [12:54:13] Found samtools - /usr/local/bin/samtools [12:54:13] Found java - /usr/local/bin/java [12:54:13] Found snpEff - /usr/local/bin/snpEff [12:54:13] Found samclip - /usr/local/bin/samclip [12:54:13] Found seqtk - /usr/local/bin/seqtk [12:54:13] Found parallel - /usr/local/bin/parallel [12:54:13] Found freebayes - /usr/local/bin/freebayes [12:54:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:54:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:54:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:54:13] Found vcfuniq - /usr/local/bin/vcfuniq [12:54:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:54:13] Found gzip - /bin/gzip [12:54:13] Found vt - /usr/local/bin/vt [12:54:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:54:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:54:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:54:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:54:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:54:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:54:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:54:14] Please supply a reference FASTA/GBK/EMBL file with --reference
2[12:58:11] This is snippy 4.6.0
Show full stderr[12:58:11] This is snippy 4.6.0 [12:58:11] Written by Torsten Seemann [12:58:11] Obtained from https://github.com/tseemann/snippy [12:58:11] Detected operating system: linux [12:58:11] Enabling bundled linux tools. [12:58:11] Found bwa - /usr/local/bin/bwa [12:58:11] Found bcftools - /usr/local/bin/bcftools [12:58:11] Found samtools - /usr/local/bin/samtools [12:58:11] Found java - /usr/local/bin/java [12:58:11] Found snpEff - /usr/local/bin/snpEff [12:58:11] Found samclip - /usr/local/bin/samclip [12:58:11] Found seqtk - /usr/local/bin/seqtk [12:58:11] Found parallel - /usr/local/bin/parallel [12:58:11] Found freebayes - /usr/local/bin/freebayes [12:58:11] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:58:11] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:58:11] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:58:11] Found vcfuniq - /usr/local/bin/vcfuniq [12:58:11] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:58:11] Found gzip - /bin/gzip [12:58:11] Found vt - /usr/local/bin/vt [12:58:11] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:58:11] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:58:11] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:58:11] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:58:11] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:58:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:58:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:58:11] Please supply a reference FASTA/GBK/EMBL file with --reference
2[12:54:57] This is snippy 4.6.0
Show full stderr[12:54:57] This is snippy 4.6.0 [12:54:57] Written by Torsten Seemann [12:54:57] Obtained from https://github.com/tseemann/snippy [12:54:57] Detected operating system: linux [12:54:57] Enabling bundled linux tools. [12:54:57] Found bwa - /usr/local/bin/bwa [12:54:57] Found bcftools - /usr/local/bin/bcftools [12:54:57] Found samtools - /usr/local/bin/samtools [12:54:57] Found java - /usr/local/bin/java [12:54:57] Found snpEff - /usr/local/bin/snpEff [12:54:57] Found samclip - /usr/local/bin/samclip [12:54:57] Found seqtk - /usr/local/bin/seqtk [12:54:57] Found parallel - /usr/local/bin/parallel [12:54:57] Found freebayes - /usr/local/bin/freebayes [12:54:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:54:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:54:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:54:57] Found vcfuniq - /usr/local/bin/vcfuniq [12:54:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:54:57] Found gzip - /bin/gzip [12:54:57] Found vt - /usr/local/bin/vt [12:54:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:54:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:54:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:54:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:54:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:54:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:54:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:54:58] Please supply a reference FASTA/GBK/EMBL file with --reference
2[12:57:43] This is snippy 4.6.0
Show full stderr[12:57:43] This is snippy 4.6.0 [12:57:43] Written by Torsten Seemann [12:57:43] Obtained from https://github.com/tseemann/snippy [12:57:43] Detected operating system: linux [12:57:43] Enabling bundled linux tools. [12:57:43] Found bwa - /usr/local/bin/bwa [12:57:43] Found bcftools - /usr/local/bin/bcftools [12:57:43] Found samtools - /usr/local/bin/samtools [12:57:43] Found java - /usr/local/bin/java [12:57:43] Found snpEff - /usr/local/bin/snpEff [12:57:43] Found samclip - /usr/local/bin/samclip [12:57:43] Found seqtk - /usr/local/bin/seqtk [12:57:43] Found parallel - /usr/local/bin/parallel [12:57:43] Found freebayes - /usr/local/bin/freebayes [12:57:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:57:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:57:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:57:43] Found vcfuniq - /usr/local/bin/vcfuniq [12:57:43] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:57:43] Found gzip - /bin/gzip [12:57:43] Found vt - /usr/local/bin/vt [12:57:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:57:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:57:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:57:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:57:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:57:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:57:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:57:44] Please supply a reference FASTA/GBK/EMBL file with --reference
2[13:04:15] This is snippy 4.6.0
Show full stderr[13:04:15] This is snippy 4.6.0 [13:04:15] Written by Torsten Seemann [13:04:15] Obtained from https://github.com/tseemann/snippy [13:04:15] Detected operating system: linux [13:04:15] Enabling bundled linux tools. [13:04:15] Found bwa - /usr/local/bin/bwa [13:04:15] Found bcftools - /usr/local/bin/bcftools [13:04:15] Found samtools - /usr/local/bin/samtools [13:04:15] Found java - /usr/local/bin/java [13:04:15] Found snpEff - /usr/local/bin/snpEff [13:04:15] Found samclip - /usr/local/bin/samclip [13:04:15] Found seqtk - /usr/local/bin/seqtk [13:04:15] Found parallel - /usr/local/bin/parallel [13:04:15] Found freebayes - /usr/local/bin/freebayes [13:04:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [13:04:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [13:04:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [13:04:15] Found vcfuniq - /usr/local/bin/vcfuniq [13:04:15] Found vcffirstheader - /usr/local/bin/vcffirstheader [13:04:15] Found gzip - /bin/gzip [13:04:15] Found vt - /usr/local/bin/vt [13:04:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [13:04:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [13:04:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [13:04:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [13:04:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [13:04:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [13:04:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [13:04:16] Please supply a reference FASTA/GBK/EMBL file with --reference
2[13:30:33] This is snippy 4.6.0
Show full stderr[13:30:33] This is snippy 4.6.0 [13:30:33] Written by Torsten Seemann [13:30:33] Obtained from https://github.com/tseemann/snippy [13:30:33] Detected operating system: linux [13:30:33] Enabling bundled linux tools. [13:30:33] Found bwa - /usr/local/bin/bwa [13:30:33] Found bcftools - /usr/local/bin/bcftools [13:30:33] Found samtools - /usr/local/bin/samtools [13:30:33] Found java - /usr/local/bin/java [13:30:33] Found snpEff - /usr/local/bin/snpEff [13:30:33] Found samclip - /usr/local/bin/samclip [13:30:33] Found seqtk - /usr/local/bin/seqtk [13:30:33] Found parallel - /usr/local/bin/parallel [13:30:33] Found freebayes - /usr/local/bin/freebayes [13:30:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [13:30:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [13:30:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [13:30:33] Found vcfuniq - /usr/local/bin/vcfuniq [13:30:33] Found vcffirstheader - /usr/local/bin/vcffirstheader [13:30:33] Found gzip - /bin/gzip [13:30:33] Found vt - /usr/local/bin/vt [13:30:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [13:30:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [13:30:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [13:30:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [13:30:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [13:30:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [13:30:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [13:30:34] Please supply a reference FASTA/GBK/EMBL file with --reference
2[12:51:27] This is snippy 4.6.0
Show full stderr[12:51:27] This is snippy 4.6.0 [12:51:27] Written by Torsten Seemann [12:51:27] Obtained from https://github.com/tseemann/snippy [12:51:27] Detected operating system: linux [12:51:27] Enabling bundled linux tools. [12:51:27] Found bwa - /usr/local/bin/bwa [12:51:27] Found bcftools - /usr/local/bin/bcftools [12:51:27] Found samtools - /usr/local/bin/samtools [12:51:27] Found java - /usr/local/bin/java [12:51:27] Found snpEff - /usr/local/bin/snpEff [12:51:27] Found samclip - /usr/local/bin/samclip [12:51:27] Found seqtk - /usr/local/bin/seqtk [12:51:27] Found parallel - /usr/local/bin/parallel [12:51:27] Found freebayes - /usr/local/bin/freebayes [12:51:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:51:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:51:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:51:27] Found vcfuniq - /usr/local/bin/vcfuniq [12:51:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:51:27] Found gzip - /bin/gzip [12:51:27] Found vt - /usr/local/bin/vt [12:51:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:51:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:51:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:51:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:51:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:51:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:51:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:51:28] Please supply a reference FASTA/GBK/EMBL file with --reference
2[12:52:07] This is snippy 4.6.0
Show full stderr[12:52:07] This is snippy 4.6.0 [12:52:07] Written by Torsten Seemann [12:52:07] Obtained from https://github.com/tseemann/snippy [12:52:07] Detected operating system: linux [12:52:07] Enabling bundled linux tools. [12:52:07] Found bwa - /usr/local/bin/bwa [12:52:07] Found bcftools - /usr/local/bin/bcftools [12:52:07] Found samtools - /usr/local/bin/samtools [12:52:07] Found java - /usr/local/bin/java [12:52:07] Found snpEff - /usr/local/bin/snpEff [12:52:07] Found samclip - /usr/local/bin/samclip [12:52:07] Found seqtk - /usr/local/bin/seqtk [12:52:07] Found parallel - /usr/local/bin/parallel [12:52:07] Found freebayes - /usr/local/bin/freebayes [12:52:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:52:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:52:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:52:07] Found vcfuniq - /usr/local/bin/vcfuniq [12:52:07] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:52:07] Found gzip - /bin/gzip [12:52:07] Found vt - /usr/local/bin/vt [12:52:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:52:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:52:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:52:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:52:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:52:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:52:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:52:08] Please supply a reference FASTA/GBK/EMBL file with --reference
2[12:52:35] This is snippy 4.6.0
Show full stderr[12:52:35] This is snippy 4.6.0 [12:52:35] Written by Torsten Seemann [12:52:35] Obtained from https://github.com/tseemann/snippy [12:52:35] Detected operating system: linux [12:52:35] Enabling bundled linux tools. [12:52:35] Found bwa - /usr/local/bin/bwa [12:52:35] Found bcftools - /usr/local/bin/bcftools [12:52:35] Found samtools - /usr/local/bin/samtools [12:52:35] Found java - /usr/local/bin/java [12:52:35] Found snpEff - /usr/local/bin/snpEff [12:52:35] Found samclip - /usr/local/bin/samclip [12:52:35] Found seqtk - /usr/local/bin/seqtk [12:52:35] Found parallel - /usr/local/bin/parallel [12:52:35] Found freebayes - /usr/local/bin/freebayes [12:52:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:52:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:52:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:52:35] Found vcfuniq - /usr/local/bin/vcfuniq [12:52:35] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:52:35] Found gzip - /bin/gzip [12:52:35] Found vt - /usr/local/bin/vt [12:52:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:52:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:52:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:52:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:52:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:52:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:52:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:52:36] Please supply a reference FASTA/GBK/EMBL file with --reference
2[12:57:57] This is snippy 4.6.0
Show full stderr[12:57:57] This is snippy 4.6.0 [12:57:57] Written by Torsten Seemann [12:57:57] Obtained from https://github.com/tseemann/snippy [12:57:57] Detected operating system: linux [12:57:57] Enabling bundled linux tools. [12:57:57] Found bwa - /usr/local/bin/bwa [12:57:57] Found bcftools - /usr/local/bin/bcftools [12:57:57] Found samtools - /usr/local/bin/samtools [12:57:57] Found java - /usr/local/bin/java [12:57:57] Found snpEff - /usr/local/bin/snpEff [12:57:57] Found samclip - /usr/local/bin/samclip [12:57:57] Found seqtk - /usr/local/bin/seqtk [12:57:57] Found parallel - /usr/local/bin/parallel [12:57:57] Found freebayes - /usr/local/bin/freebayes [12:57:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:57:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:57:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:57:57] Found vcfuniq - /usr/local/bin/vcfuniq [12:57:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:57:57] Found gzip - /bin/gzip [12:57:57] Found vt - /usr/local/bin/vt [12:57:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:57:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:57:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:57:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:57:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:57:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:57:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:57:57] Please supply a reference FASTA/GBK/EMBL file with --reference
2[12:59:05] This is snippy 4.6.0
Show full stderr[12:59:05] This is snippy 4.6.0 [12:59:05] Written by Torsten Seemann [12:59:05] Obtained from https://github.com/tseemann/snippy [12:59:05] Detected operating system: linux [12:59:05] Enabling bundled linux tools. [12:59:05] Found bwa - /usr/local/bin/bwa [12:59:05] Found bcftools - /usr/local/bin/bcftools [12:59:05] Found samtools - /usr/local/bin/samtools [12:59:05] Found java - /usr/local/bin/java [12:59:05] Found snpEff - /usr/local/bin/snpEff [12:59:05] Found samclip - /usr/local/bin/samclip [12:59:05] Found seqtk - /usr/local/bin/seqtk [12:59:05] Found parallel - /usr/local/bin/parallel [12:59:05] Found freebayes - /usr/local/bin/freebayes [12:59:05] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:59:05] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:59:05] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:59:05] Found vcfuniq - /usr/local/bin/vcfuniq [12:59:05] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:59:05] Found gzip - /bin/gzip [12:59:05] Found vt - /usr/local/bin/vt [12:59:05] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:59:05] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:59:05] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:59:05] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:59:05] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:59:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:59:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:59:06] Please supply a reference FASTA/GBK/EMBL file with --reference
2[12:59:21] This is snippy 4.6.0
Show full stderr[12:59:21] This is snippy 4.6.0 [12:59:21] Written by Torsten Seemann [12:59:21] Obtained from https://github.com/tseemann/snippy [12:59:21] Detected operating system: linux [12:59:21] Enabling bundled linux tools. [12:59:21] Found bwa - /usr/local/bin/bwa [12:59:21] Found bcftools - /usr/local/bin/bcftools [12:59:21] Found samtools - /usr/local/bin/samtools [12:59:21] Found java - /usr/local/bin/java [12:59:21] Found snpEff - /usr/local/bin/snpEff [12:59:21] Found samclip - /usr/local/bin/samclip [12:59:21] Found seqtk - /usr/local/bin/seqtk [12:59:21] Found parallel - /usr/local/bin/parallel [12:59:21] Found freebayes - /usr/local/bin/freebayes [12:59:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:59:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:59:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:59:21] Found vcfuniq - /usr/local/bin/vcfuniq [12:59:21] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:59:21] Found gzip - /bin/gzip [12:59:21] Found vt - /usr/local/bin/vt [12:59:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:59:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:59:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:59:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:59:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:59:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:59:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:59:22] Please supply a reference FASTA/GBK/EMBL file with --reference
2[12:59:18] This is snippy 4.6.0
Show full stderr[12:59:18] This is snippy 4.6.0 [12:59:18] Written by Torsten Seemann [12:59:18] Obtained from https://github.com/tseemann/snippy [12:59:18] Detected operating system: linux [12:59:18] Enabling bundled linux tools. [12:59:18] Found bwa - /usr/local/bin/bwa [12:59:18] Found bcftools - /usr/local/bin/bcftools [12:59:18] Found samtools - /usr/local/bin/samtools [12:59:18] Found java - /usr/local/bin/java [12:59:18] Found snpEff - /usr/local/bin/snpEff [12:59:18] Found samclip - /usr/local/bin/samclip [12:59:18] Found seqtk - /usr/local/bin/seqtk [12:59:18] Found parallel - /usr/local/bin/parallel [12:59:18] Found freebayes - /usr/local/bin/freebayes [12:59:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:59:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:59:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:59:18] Found vcfuniq - /usr/local/bin/vcfuniq [12:59:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:59:18] Found gzip - /bin/gzip [12:59:18] Found vt - /usr/local/bin/vt [12:59:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:59:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:59:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:59:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:59:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:59:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:59:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:59:19] Please supply a reference FASTA/GBK/EMBL file with --reference
2[12:59:49] This is snippy 4.6.0
Show full stderr[12:59:49] This is snippy 4.6.0 [12:59:49] Written by Torsten Seemann [12:59:49] Obtained from https://github.com/tseemann/snippy [12:59:49] Detected operating system: linux [12:59:49] Enabling bundled linux tools. [12:59:49] Found bwa - /usr/local/bin/bwa [12:59:49] Found bcftools - /usr/local/bin/bcftools [12:59:49] Found samtools - /usr/local/bin/samtools [12:59:49] Found java - /usr/local/bin/java [12:59:49] Found snpEff - /usr/local/bin/snpEff [12:59:49] Found samclip - /usr/local/bin/samclip [12:59:49] Found seqtk - /usr/local/bin/seqtk [12:59:49] Found parallel - /usr/local/bin/parallel [12:59:49] Found freebayes - /usr/local/bin/freebayes [12:59:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:59:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:59:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:59:49] Found vcfuniq - /usr/local/bin/vcfuniq [12:59:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:59:49] Found gzip - /bin/gzip [12:59:49] Found vt - /usr/local/bin/vt [12:59:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:59:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:59:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:59:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:59:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:59:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:59:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:59:50] Please supply a reference FASTA/GBK/EMBL file with --reference
2[16:31:37] This is snippy 4.6.0
Show full stderr[16:31:37] This is snippy 4.6.0 [16:31:37] Written by Torsten Seemann [16:31:37] Obtained from https://github.com/tseemann/snippy [16:31:37] Detected operating system: linux [16:31:37] Enabling bundled linux tools. [16:31:37] Found bwa - /usr/local/bin/bwa [16:31:37] Found bcftools - /usr/local/bin/bcftools [16:31:37] Found samtools - /usr/local/bin/samtools [16:31:37] Found java - /usr/local/bin/java [16:31:37] Found snpEff - /usr/local/bin/snpEff [16:31:37] Found samclip - /usr/local/bin/samclip [16:31:37] Found seqtk - /usr/local/bin/seqtk [16:31:37] Found parallel - /usr/local/bin/parallel [16:31:37] Found freebayes - /usr/local/bin/freebayes [16:31:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [16:31:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [16:31:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [16:31:37] Found vcfuniq - /usr/local/bin/vcfuniq [16:31:37] Found vcffirstheader - /usr/local/bin/vcffirstheader [16:31:37] Found gzip - /bin/gzip [16:31:37] Found vt - /usr/local/bin/vt [16:31:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [16:31:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [16:31:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [16:31:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [16:31:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [16:31:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [16:31:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [16:31:37] Please supply a reference FASTA/GBK/EMBL file with --reference
2[19:40:28] This is snippy 4.6.0
Show full stderr[19:40:28] This is snippy 4.6.0 [19:40:28] Written by Torsten Seemann [19:40:28] Obtained from https://github.com/tseemann/snippy [19:40:28] Detected operating system: linux [19:40:28] Enabling bundled linux tools. [19:40:28] Found bwa - /usr/local/bin/bwa [19:40:28] Found bcftools - /usr/local/bin/bcftools [19:40:28] Found samtools - /usr/local/bin/samtools [19:40:28] Found java - /usr/local/bin/java [19:40:28] Found snpEff - /usr/local/bin/snpEff [19:40:28] Found samclip - /usr/local/bin/samclip [19:40:28] Found seqtk - /usr/local/bin/seqtk [19:40:28] Found parallel - /usr/local/bin/parallel [19:40:28] Found freebayes - /usr/local/bin/freebayes [19:40:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [19:40:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [19:40:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [19:40:28] Found vcfuniq - /usr/local/bin/vcfuniq [19:40:28] Found vcffirstheader - /usr/local/bin/vcffirstheader [19:40:28] Found gzip - /bin/gzip [19:40:28] Found vt - /usr/local/bin/vt [19:40:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [19:40:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [19:40:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [19:40:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [19:40:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [19:40:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [19:40:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [19:40:28] Please supply a reference FASTA/GBK/EMBL file with --reference
2[19:40:55] This is snippy 4.6.0
Show full stderr[19:40:55] This is snippy 4.6.0 [19:40:55] Written by Torsten Seemann [19:40:55] Obtained from https://github.com/tseemann/snippy [19:40:55] Detected operating system: linux [19:40:55] Enabling bundled linux tools. [19:40:55] Found bwa - /usr/local/bin/bwa [19:40:55] Found bcftools - /usr/local/bin/bcftools [19:40:55] Found samtools - /usr/local/bin/samtools [19:40:55] Found java - /usr/local/bin/java [19:40:55] Found snpEff - /usr/local/bin/snpEff [19:40:55] Found samclip - /usr/local/bin/samclip [19:40:55] Found seqtk - /usr/local/bin/seqtk [19:40:55] Found parallel - /usr/local/bin/parallel [19:40:55] Found freebayes - /usr/local/bin/freebayes [19:40:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [19:40:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [19:40:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [19:40:55] Found vcfuniq - /usr/local/bin/vcfuniq [19:40:55] Found vcffirstheader - /usr/local/bin/vcffirstheader [19:40:55] Found gzip - /bin/gzip [19:40:55] Found vt - /usr/local/bin/vt [19:40:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [19:40:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [19:40:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [19:40:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [19:40:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [19:40:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [19:40:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [19:40:56] Please supply a reference FASTA/GBK/EMBL file with --reference
2[19:40:47] This is snippy 4.6.0
Show full stderr[19:40:47] This is snippy 4.6.0 [19:40:47] Written by Torsten Seemann [19:40:47] Obtained from https://github.com/tseemann/snippy [19:40:47] Detected operating system: linux [19:40:47] Enabling bundled linux tools. [19:40:47] Found bwa - /usr/local/bin/bwa [19:40:47] Found bcftools - /usr/local/bin/bcftools [19:40:47] Found samtools - /usr/local/bin/samtools [19:40:47] Found java - /usr/local/bin/java [19:40:47] Found snpEff - /usr/local/bin/snpEff [19:40:47] Found samclip - /usr/local/bin/samclip [19:40:47] Found seqtk - /usr/local/bin/seqtk [19:40:47] Found parallel - /usr/local/bin/parallel [19:40:47] Found freebayes - /usr/local/bin/freebayes [19:40:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [19:40:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [19:40:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [19:40:47] Found vcfuniq - /usr/local/bin/vcfuniq [19:40:47] Found vcffirstheader - /usr/local/bin/vcffirstheader [19:40:47] Found gzip - /bin/gzip [19:40:47] Found vt - /usr/local/bin/vt [19:40:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [19:40:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [19:40:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [19:40:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [19:40:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [19:40:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [19:40:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [19:40:48] Please supply a reference FASTA/GBK/EMBL file with --reference
2[08:48:47] This is snippy 4.6.0
Show full stderr[08:48:47] This is snippy 4.6.0 [08:48:47] Written by Torsten Seemann [08:48:47] Obtained from https://github.com/tseemann/snippy [08:48:47] Detected operating system: linux [08:48:47] Enabling bundled linux tools. [08:48:47] Found bwa - /usr/local/bin/bwa [08:48:47] Found bcftools - /usr/local/bin/bcftools [08:48:47] Found samtools - /usr/local/bin/samtools [08:48:47] Found java - /usr/local/bin/java [08:48:47] Found snpEff - /usr/local/bin/snpEff [08:48:47] Found samclip - /usr/local/bin/samclip [08:48:47] Found seqtk - /usr/local/bin/seqtk [08:48:47] Found parallel - /usr/local/bin/parallel [08:48:47] Found freebayes - /usr/local/bin/freebayes [08:48:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:48:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:48:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:48:48] Found vcfuniq - /usr/local/bin/vcfuniq [08:48:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:48:48] Found gzip - /bin/gzip [08:48:48] Found vt - /usr/local/bin/vt [08:48:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:48:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:48:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:48:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:48:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:48:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:48:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:48:49] Please supply a reference FASTA/GBK/EMBL file with --reference
2[09:02:02] This is snippy 4.6.0
Show full stderr[09:02:02] This is snippy 4.6.0 [09:02:02] Written by Torsten Seemann [09:02:02] Obtained from https://github.com/tseemann/snippy [09:02:02] Detected operating system: linux [09:02:02] Enabling bundled linux tools. [09:02:02] Found bwa - /usr/local/bin/bwa [09:02:02] Found bcftools - /usr/local/bin/bcftools [09:02:02] Found samtools - /usr/local/bin/samtools [09:02:02] Found java - /usr/local/bin/java [09:02:02] Found snpEff - /usr/local/bin/snpEff [09:02:02] Found samclip - /usr/local/bin/samclip [09:02:02] Found seqtk - /usr/local/bin/seqtk [09:02:02] Found parallel - /usr/local/bin/parallel [09:02:02] Found freebayes - /usr/local/bin/freebayes [09:02:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [09:02:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [09:02:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [09:02:02] Found vcfuniq - /usr/local/bin/vcfuniq [09:02:02] Found vcffirstheader - /usr/local/bin/vcffirstheader [09:02:02] Found gzip - /bin/gzip [09:02:02] Found vt - /usr/local/bin/vt [09:02:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [09:02:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [09:02:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [09:02:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [09:02:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [09:02:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [09:02:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [09:02:03] Please supply a reference FASTA/GBK/EMBL file with --reference
2[14:45:05] This is snippy 4.6.0
Show full stderr[14:45:05] This is snippy 4.6.0 [14:45:05] Written by Torsten Seemann [14:45:05] Obtained from https://github.com/tseemann/snippy [14:45:05] Detected operating system: linux [14:45:05] Enabling bundled linux tools. [14:45:05] Found bwa - /usr/local/bin/bwa [14:45:05] Found bcftools - /usr/local/bin/bcftools [14:45:05] Found samtools - /usr/local/bin/samtools [14:45:05] Found java - /usr/local/bin/java [14:45:05] Found snpEff - /usr/local/bin/snpEff [14:45:05] Found samclip - /usr/local/bin/samclip [14:45:05] Found seqtk - /usr/local/bin/seqtk [14:45:05] Found parallel - /usr/local/bin/parallel [14:45:05] Found freebayes - /usr/local/bin/freebayes [14:45:05] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:45:05] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:45:05] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:45:05] Found vcfuniq - /usr/local/bin/vcfuniq [14:45:05] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:45:05] Found gzip - /bin/gzip [14:45:05] Found vt - /usr/local/bin/vt [14:45:05] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:45:05] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:45:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:45:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:45:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:45:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:45:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:45:07] Please supply a reference FASTA/GBK/EMBL file with --reference
2[14:45:18] This is snippy 4.6.0
Show full stderr[14:45:18] This is snippy 4.6.0 [14:45:18] Written by Torsten Seemann [14:45:18] Obtained from https://github.com/tseemann/snippy [14:45:18] Detected operating system: linux [14:45:18] Enabling bundled linux tools. [14:45:18] Found bwa - /usr/local/bin/bwa [14:45:18] Found bcftools - /usr/local/bin/bcftools [14:45:18] Found samtools - /usr/local/bin/samtools [14:45:18] Found java - /usr/local/bin/java [14:45:18] Found snpEff - /usr/local/bin/snpEff [14:45:18] Found samclip - /usr/local/bin/samclip [14:45:18] Found seqtk - /usr/local/bin/seqtk [14:45:18] Found parallel - /usr/local/bin/parallel [14:45:18] Found freebayes - /usr/local/bin/freebayes [14:45:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:45:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:45:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:45:18] Found vcfuniq - /usr/local/bin/vcfuniq [14:45:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:45:18] Found gzip - /bin/gzip [14:45:18] Found vt - /usr/local/bin/vt [14:45:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:45:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:45:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:45:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:45:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:45:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:45:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:45:19] Please supply a reference FASTA/GBK/EMBL file with --reference
2[14:45:45] This is snippy 4.6.0
Show full stderr[14:45:45] This is snippy 4.6.0 [14:45:45] Written by Torsten Seemann [14:45:45] Obtained from https://github.com/tseemann/snippy [14:45:45] Detected operating system: linux [14:45:45] Enabling bundled linux tools. [14:45:45] Found bwa - /usr/local/bin/bwa [14:45:45] Found bcftools - /usr/local/bin/bcftools [14:45:45] Found samtools - /usr/local/bin/samtools [14:45:45] Found java - /usr/local/bin/java [14:45:45] Found snpEff - /usr/local/bin/snpEff [14:45:45] Found samclip - /usr/local/bin/samclip [14:45:45] Found seqtk - /usr/local/bin/seqtk [14:45:45] Found parallel - /usr/local/bin/parallel [14:45:45] Found freebayes - /usr/local/bin/freebayes [14:45:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:45:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:45:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:45:45] Found vcfuniq - /usr/local/bin/vcfuniq [14:45:45] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:45:45] Found gzip - /bin/gzip [14:45:45] Found vt - /usr/local/bin/vt [14:45:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:45:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:45:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:45:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:45:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:45:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:45:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:45:46] Please supply a reference FASTA/GBK/EMBL file with --reference
2[14:46:03] This is snippy 4.6.0
Show full stderr[14:46:03] This is snippy 4.6.0 [14:46:03] Written by Torsten Seemann [14:46:03] Obtained from https://github.com/tseemann/snippy [14:46:03] Detected operating system: linux [14:46:03] Enabling bundled linux tools. [14:46:03] Found bwa - /usr/local/bin/bwa [14:46:03] Found bcftools - /usr/local/bin/bcftools [14:46:03] Found samtools - /usr/local/bin/samtools [14:46:04] Found java - /usr/local/bin/java [14:46:04] Found snpEff - /usr/local/bin/snpEff [14:46:04] Found samclip - /usr/local/bin/samclip [14:46:04] Found seqtk - /usr/local/bin/seqtk [14:46:04] Found parallel - /usr/local/bin/parallel [14:46:04] Found freebayes - /usr/local/bin/freebayes [14:46:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:46:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:46:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:46:04] Found vcfuniq - /usr/local/bin/vcfuniq [14:46:04] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:46:04] Found gzip - /bin/gzip [14:46:04] Found vt - /usr/local/bin/vt [14:46:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:46:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:46:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:46:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:46:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:46:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:46:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:46:05] Please supply a reference FASTA/GBK/EMBL file with --reference
2[14:45:30] This is snippy 4.6.0
Show full stderr[14:45:30] This is snippy 4.6.0 [14:45:30] Written by Torsten Seemann [14:45:30] Obtained from https://github.com/tseemann/snippy [14:45:30] Detected operating system: linux [14:45:30] Enabling bundled linux tools. [14:45:30] Found bwa - /usr/local/bin/bwa [14:45:30] Found bcftools - /usr/local/bin/bcftools [14:45:30] Found samtools - /usr/local/bin/samtools [14:45:30] Found java - /usr/local/bin/java [14:45:30] Found snpEff - /usr/local/bin/snpEff [14:45:30] Found samclip - /usr/local/bin/samclip [14:45:30] Found seqtk - /usr/local/bin/seqtk [14:45:30] Found parallel - /usr/local/bin/parallel [14:45:30] Found freebayes - /usr/local/bin/freebayes [14:45:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:45:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:45:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:45:30] Found vcfuniq - /usr/local/bin/vcfuniq [14:45:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:45:30] Found gzip - /bin/gzip [14:45:30] Found vt - /usr/local/bin/vt [14:45:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:45:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:45:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:45:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:45:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:45:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:45:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:45:31] Please supply a reference FASTA/GBK/EMBL file with --reference
2[14:45:33] This is snippy 4.6.0
Show full stderr[14:45:33] This is snippy 4.6.0 [14:45:33] Written by Torsten Seemann [14:45:33] Obtained from https://github.com/tseemann/snippy [14:45:33] Detected operating system: linux [14:45:33] Enabling bundled linux tools. [14:45:33] Found bwa - /usr/local/bin/bwa [14:45:33] Found bcftools - /usr/local/bin/bcftools [14:45:33] Found samtools - /usr/local/bin/samtools [14:45:33] Found java - /usr/local/bin/java [14:45:33] Found snpEff - /usr/local/bin/snpEff [14:45:33] Found samclip - /usr/local/bin/samclip [14:45:33] Found seqtk - /usr/local/bin/seqtk [14:45:33] Found parallel - /usr/local/bin/parallel [14:45:33] Found freebayes - /usr/local/bin/freebayes [14:45:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:45:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:45:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:45:33] Found vcfuniq - /usr/local/bin/vcfuniq [14:45:33] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:45:33] Found gzip - /bin/gzip [14:45:33] Found vt - /usr/local/bin/vt [14:45:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:45:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:45:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:45:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:45:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:45:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:45:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:45:34] Please supply a reference FASTA/GBK/EMBL file with --reference
2[14:45:48] This is snippy 4.6.0
Show full stderr[14:45:48] This is snippy 4.6.0 [14:45:48] Written by Torsten Seemann [14:45:48] Obtained from https://github.com/tseemann/snippy [14:45:48] Detected operating system: linux [14:45:48] Enabling bundled linux tools. [14:45:48] Found bwa - /usr/local/bin/bwa [14:45:48] Found bcftools - /usr/local/bin/bcftools [14:45:48] Found samtools - /usr/local/bin/samtools [14:45:48] Found java - /usr/local/bin/java [14:45:48] Found snpEff - /usr/local/bin/snpEff [14:45:48] Found samclip - /usr/local/bin/samclip [14:45:48] Found seqtk - /usr/local/bin/seqtk [14:45:48] Found parallel - /usr/local/bin/parallel [14:45:48] Found freebayes - /usr/local/bin/freebayes [14:45:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:45:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:45:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:45:48] Found vcfuniq - /usr/local/bin/vcfuniq [14:45:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:45:48] Found gzip - /bin/gzip [14:45:48] Found vt - /usr/local/bin/vt [14:45:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:45:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:45:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:45:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:45:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:45:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:45:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:45:49] Please supply a reference FASTA/GBK/EMBL file with --reference
2[14:45:54] This is snippy 4.6.0
Show full stderr[14:45:54] This is snippy 4.6.0 [14:45:54] Written by Torsten Seemann [14:45:54] Obtained from https://github.com/tseemann/snippy [14:45:54] Detected operating system: linux [14:45:54] Enabling bundled linux tools. [14:45:54] Found bwa - /usr/local/bin/bwa [14:45:54] Found bcftools - /usr/local/bin/bcftools [14:45:54] Found samtools - /usr/local/bin/samtools [14:45:54] Found java - /usr/local/bin/java [14:45:54] Found snpEff - /usr/local/bin/snpEff [14:45:54] Found samclip - /usr/local/bin/samclip [14:45:54] Found seqtk - /usr/local/bin/seqtk [14:45:54] Found parallel - /usr/local/bin/parallel [14:45:54] Found freebayes - /usr/local/bin/freebayes [14:45:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:45:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:45:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:45:54] Found vcfuniq - /usr/local/bin/vcfuniq [14:45:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:45:54] Found gzip - /bin/gzip [14:45:54] Found vt - /usr/local/bin/vt [14:45:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:45:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:45:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:45:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:45:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:45:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:45:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:45:55] Please supply a reference FASTA/GBK/EMBL file with --reference
2[14:50:57] This is snippy 4.6.0
Show full stderr[14:50:57] This is snippy 4.6.0 [14:50:57] Written by Torsten Seemann [14:50:57] Obtained from https://github.com/tseemann/snippy [14:50:57] Detected operating system: linux [14:50:57] Enabling bundled linux tools. [14:50:57] Found bwa - /usr/local/bin/bwa [14:50:57] Found bcftools - /usr/local/bin/bcftools [14:50:57] Found samtools - /usr/local/bin/samtools [14:50:57] Found java - /usr/local/bin/java [14:50:57] Found snpEff - /usr/local/bin/snpEff [14:50:57] Found samclip - /usr/local/bin/samclip [14:50:57] Found seqtk - /usr/local/bin/seqtk [14:50:57] Found parallel - /usr/local/bin/parallel [14:50:57] Found freebayes - /usr/local/bin/freebayes [14:50:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:50:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:50:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:50:57] Found vcfuniq - /usr/local/bin/vcfuniq [14:50:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:50:57] Found gzip - /bin/gzip [14:50:57] Found vt - /usr/local/bin/vt [14:50:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:50:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:50:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:50:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:50:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:50:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:50:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:50:58] Please supply a reference FASTA/GBK/EMBL file with --reference
2[14:44:57] This is snippy 4.6.0
Show full stderr[14:44:57] This is snippy 4.6.0 [14:44:57] Written by Torsten Seemann [14:44:57] Obtained from https://github.com/tseemann/snippy [14:44:57] Detected operating system: linux [14:44:57] Enabling bundled linux tools. [14:44:57] Found bwa - /usr/local/bin/bwa [14:44:57] Found bcftools - /usr/local/bin/bcftools [14:44:57] Found samtools - /usr/local/bin/samtools [14:44:57] Found java - /usr/local/bin/java [14:44:57] Found snpEff - /usr/local/bin/snpEff [14:44:57] Found samclip - /usr/local/bin/samclip [14:44:57] Found seqtk - /usr/local/bin/seqtk [14:44:57] Found parallel - /usr/local/bin/parallel [14:44:57] Found freebayes - /usr/local/bin/freebayes [14:44:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:44:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:44:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:44:57] Found vcfuniq - /usr/local/bin/vcfuniq [14:44:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:44:57] Found gzip - /bin/gzip [14:44:57] Found vt - /usr/local/bin/vt [14:44:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:44:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:44:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:44:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:44:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:44:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:44:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:44:58] Please supply a reference FASTA/GBK/EMBL file with --reference
2[14:46:58] This is snippy 4.6.0
Show full stderr[14:46:58] This is snippy 4.6.0 [14:46:58] Written by Torsten Seemann [14:46:58] Obtained from https://github.com/tseemann/snippy [14:46:58] Detected operating system: linux [14:46:58] Enabling bundled linux tools. [14:46:58] Found bwa - /usr/local/bin/bwa [14:46:58] Found bcftools - /usr/local/bin/bcftools [14:46:58] Found samtools - /usr/local/bin/samtools [14:46:58] Found java - /usr/local/bin/java [14:46:58] Found snpEff - /usr/local/bin/snpEff [14:46:59] Found samclip - /usr/local/bin/samclip [14:46:59] Found seqtk - /usr/local/bin/seqtk [14:46:59] Found parallel - /usr/local/bin/parallel [14:46:59] Found freebayes - /usr/local/bin/freebayes [14:46:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:46:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:46:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:46:59] Found vcfuniq - /usr/local/bin/vcfuniq [14:46:59] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:46:59] Found gzip - /bin/gzip [14:46:59] Found vt - /usr/local/bin/vt [14:46:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:46:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:46:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:46:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:46:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:47:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:47:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:47:00] Please supply a reference FASTA/GBK/EMBL file with --reference
2[14:57:56] This is snippy 4.6.0
Show full stderr[14:57:56] This is snippy 4.6.0 [14:57:56] Written by Torsten Seemann [14:57:56] Obtained from https://github.com/tseemann/snippy [14:57:56] Detected operating system: linux [14:57:56] Enabling bundled linux tools. [14:57:56] Found bwa - /usr/local/bin/bwa [14:57:56] Found bcftools - /usr/local/bin/bcftools [14:57:56] Found samtools - /usr/local/bin/samtools [14:57:56] Found java - /usr/local/bin/java [14:57:56] Found snpEff - /usr/local/bin/snpEff [14:57:56] Found samclip - /usr/local/bin/samclip [14:57:56] Found seqtk - /usr/local/bin/seqtk [14:57:56] Found parallel - /usr/local/bin/parallel [14:57:56] Found freebayes - /usr/local/bin/freebayes [14:57:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:57:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:57:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:57:56] Found vcfuniq - /usr/local/bin/vcfuniq [14:57:56] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:57:56] Found gzip - /bin/gzip [14:57:56] Found vt - /usr/local/bin/vt [14:57:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:57:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:57:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:57:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:57:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:57:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:57:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:57:56] Please supply a reference FASTA/GBK/EMBL file with --reference
2[15:02:56] This is snippy 4.6.0
Show full stderr[15:02:56] This is snippy 4.6.0 [15:02:56] Written by Torsten Seemann [15:02:56] Obtained from https://github.com/tseemann/snippy [15:02:56] Detected operating system: linux [15:02:56] Enabling bundled linux tools. [15:02:56] Found bwa - /usr/local/bin/bwa [15:02:56] Found bcftools - /usr/local/bin/bcftools [15:02:56] Found samtools - /usr/local/bin/samtools [15:02:56] Found java - /usr/local/bin/java [15:02:56] Found snpEff - /usr/local/bin/snpEff [15:02:56] Found samclip - /usr/local/bin/samclip [15:02:56] Found seqtk - /usr/local/bin/seqtk [15:02:56] Found parallel - /usr/local/bin/parallel [15:02:56] Found freebayes - /usr/local/bin/freebayes [15:02:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [15:02:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [15:02:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [15:02:56] Found vcfuniq - /usr/local/bin/vcfuniq [15:02:56] Found vcffirstheader - /usr/local/bin/vcffirstheader [15:02:56] Found gzip - /bin/gzip [15:02:56] Found vt - /usr/local/bin/vt [15:02:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [15:02:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [15:02:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [15:02:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [15:02:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [15:02:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [15:02:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [15:02:57] Please supply a reference FASTA/GBK/EMBL file with --reference
2[14:46:57] This is snippy 4.6.0
Show full stderr[14:46:57] This is snippy 4.6.0 [14:46:57] Written by Torsten Seemann [14:46:57] Obtained from https://github.com/tseemann/snippy [14:46:57] Detected operating system: linux [14:46:57] Enabling bundled linux tools. [14:46:57] Found bwa - /usr/local/bin/bwa [14:46:57] Found bcftools - /usr/local/bin/bcftools [14:46:57] Found samtools - /usr/local/bin/samtools [14:46:57] Found java - /usr/local/bin/java [14:46:57] Found snpEff - /usr/local/bin/snpEff [14:46:57] Found samclip - /usr/local/bin/samclip [14:46:57] Found seqtk - /usr/local/bin/seqtk [14:46:57] Found parallel - /usr/local/bin/parallel [14:46:57] Found freebayes - /usr/local/bin/freebayes [14:46:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:46:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:46:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:46:58] Found vcfuniq - /usr/local/bin/vcfuniq [14:46:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:46:58] Found gzip - /bin/gzip [14:46:58] Found vt - /usr/local/bin/vt [14:46:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:46:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:46:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:46:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:46:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:46:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:46:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:46:58] Please supply a reference FASTA/GBK/EMBL file with --reference
2[15:14:57] This is snippy 4.6.0
Show full stderr[15:14:57] This is snippy 4.6.0 [15:14:57] Written by Torsten Seemann [15:14:57] Obtained from https://github.com/tseemann/snippy [15:14:57] Detected operating system: linux [15:14:57] Enabling bundled linux tools. [15:14:57] Found bwa - /usr/local/bin/bwa [15:14:57] Found bcftools - /usr/local/bin/bcftools [15:14:57] Found samtools - /usr/local/bin/samtools [15:14:57] Found java - /usr/local/bin/java [15:14:57] Found snpEff - /usr/local/bin/snpEff [15:14:57] Found samclip - /usr/local/bin/samclip [15:14:57] Found seqtk - /usr/local/bin/seqtk [15:14:57] Found parallel - /usr/local/bin/parallel [15:14:57] Found freebayes - /usr/local/bin/freebayes [15:14:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [15:14:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [15:14:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [15:14:57] Found vcfuniq - /usr/local/bin/vcfuniq [15:14:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [15:14:57] Found gzip - /bin/gzip [15:14:57] Found vt - /usr/local/bin/vt [15:14:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [15:14:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [15:14:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [15:14:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [15:14:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [15:14:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [15:14:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [15:14:59] Please supply a reference FASTA/GBK/EMBL file with --reference
2[14:46:18] This is snippy 4.6.0
Show full stderr[14:46:18] This is snippy 4.6.0 [14:46:18] Written by Torsten Seemann [14:46:18] Obtained from https://github.com/tseemann/snippy [14:46:18] Detected operating system: linux [14:46:18] Enabling bundled linux tools. [14:46:18] Found bwa - /usr/local/bin/bwa [14:46:18] Found bcftools - /usr/local/bin/bcftools [14:46:18] Found samtools - /usr/local/bin/samtools [14:46:18] Found java - /usr/local/bin/java [14:46:18] Found snpEff - /usr/local/bin/snpEff [14:46:18] Found samclip - /usr/local/bin/samclip [14:46:18] Found seqtk - /usr/local/bin/seqtk [14:46:18] Found parallel - /usr/local/bin/parallel [14:46:18] Found freebayes - /usr/local/bin/freebayes [14:46:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:46:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:46:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:46:18] Found vcfuniq - /usr/local/bin/vcfuniq [14:46:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:46:18] Found gzip - /bin/gzip [14:46:18] Found vt - /usr/local/bin/vt [14:46:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:46:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:46:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:46:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:46:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:46:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:46:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:46:19] Please supply a reference FASTA/GBK/EMBL file with --reference
2[14:48:42] This is snippy 4.6.0
Show full stderr[14:48:42] This is snippy 4.6.0 [14:48:42] Written by Torsten Seemann [14:48:42] Obtained from https://github.com/tseemann/snippy [14:48:42] Detected operating system: linux [14:48:42] Enabling bundled linux tools. [14:48:42] Found bwa - /usr/local/bin/bwa [14:48:42] Found bcftools - /usr/local/bin/bcftools [14:48:42] Found samtools - /usr/local/bin/samtools [14:48:42] Found java - /usr/local/bin/java [14:48:42] Found snpEff - /usr/local/bin/snpEff [14:48:42] Found samclip - /usr/local/bin/samclip [14:48:42] Found seqtk - /usr/local/bin/seqtk [14:48:42] Found parallel - /usr/local/bin/parallel [14:48:42] Found freebayes - /usr/local/bin/freebayes [14:48:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:48:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:48:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:48:42] Found vcfuniq - /usr/local/bin/vcfuniq [14:48:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:48:42] Found gzip - /bin/gzip [14:48:42] Found vt - /usr/local/bin/vt [14:48:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:48:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:48:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:48:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:48:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:48:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:48:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:48:43] Please supply a reference FASTA/GBK/EMBL file with --reference
2[14:48:03] This is snippy 4.6.0
Show full stderr[14:48:03] This is snippy 4.6.0 [14:48:03] Written by Torsten Seemann [14:48:03] Obtained from https://github.com/tseemann/snippy [14:48:03] Detected operating system: linux [14:48:03] Enabling bundled linux tools. [14:48:03] Found bwa - /usr/local/bin/bwa [14:48:03] Found bcftools - /usr/local/bin/bcftools [14:48:03] Found samtools - /usr/local/bin/samtools [14:48:03] Found java - /usr/local/bin/java [14:48:03] Found snpEff - /usr/local/bin/snpEff [14:48:03] Found samclip - /usr/local/bin/samclip [14:48:03] Found seqtk - /usr/local/bin/seqtk [14:48:03] Found parallel - /usr/local/bin/parallel [14:48:03] Found freebayes - /usr/local/bin/freebayes [14:48:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:48:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:48:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:48:03] Found vcfuniq - /usr/local/bin/vcfuniq [14:48:03] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:48:03] Found gzip - /bin/gzip [14:48:03] Found vt - /usr/local/bin/vt [14:48:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:48:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:48:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:48:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:48:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:48:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:48:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:48:04] Please supply a reference FASTA/GBK/EMBL file with --reference
2[14:47:51] This is snippy 4.6.0
Show full stderr[14:47:51] This is snippy 4.6.0 [14:47:51] Written by Torsten Seemann [14:47:51] Obtained from https://github.com/tseemann/snippy [14:47:51] Detected operating system: linux [14:47:51] Enabling bundled linux tools. [14:47:51] Found bwa - /usr/local/bin/bwa [14:47:51] Found bcftools - /usr/local/bin/bcftools [14:47:51] Found samtools - /usr/local/bin/samtools [14:47:51] Found java - /usr/local/bin/java [14:47:51] Found snpEff - /usr/local/bin/snpEff [14:47:51] Found samclip - /usr/local/bin/samclip [14:47:51] Found seqtk - /usr/local/bin/seqtk [14:47:51] Found parallel - /usr/local/bin/parallel [14:47:51] Found freebayes - /usr/local/bin/freebayes [14:47:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:47:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:47:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:47:51] Found vcfuniq - /usr/local/bin/vcfuniq [14:47:51] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:47:51] Found gzip - /bin/gzip [14:47:51] Found vt - /usr/local/bin/vt [14:47:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:47:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:47:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:47:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:47:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:47:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:47:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:47:52] Please supply a reference FASTA/GBK/EMBL file with --reference
2[14:48:57] This is snippy 4.6.0
Show full stderr[14:48:57] This is snippy 4.6.0 [14:48:57] Written by Torsten Seemann [14:48:57] Obtained from https://github.com/tseemann/snippy [14:48:57] Detected operating system: linux [14:48:57] Enabling bundled linux tools. [14:48:57] Found bwa - /usr/local/bin/bwa [14:48:57] Found bcftools - /usr/local/bin/bcftools [14:48:57] Found samtools - /usr/local/bin/samtools [14:48:57] Found java - /usr/local/bin/java [14:48:57] Found snpEff - /usr/local/bin/snpEff [14:48:57] Found samclip - /usr/local/bin/samclip [14:48:57] Found seqtk - /usr/local/bin/seqtk [14:48:57] Found parallel - /usr/local/bin/parallel [14:48:57] Found freebayes - /usr/local/bin/freebayes [14:48:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:48:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:48:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:48:57] Found vcfuniq - /usr/local/bin/vcfuniq [14:48:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:48:57] Found gzip - /bin/gzip [14:48:57] Found vt - /usr/local/bin/vt [14:48:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:48:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:48:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:48:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:48:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:48:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:48:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:48:58] Please supply a reference FASTA/GBK/EMBL file with --reference
2[14:49:26] This is snippy 4.6.0
Show full stderr[14:49:26] This is snippy 4.6.0 [14:49:26] Written by Torsten Seemann [14:49:26] Obtained from https://github.com/tseemann/snippy [14:49:26] Detected operating system: linux [14:49:26] Enabling bundled linux tools. [14:49:26] Found bwa - /usr/local/bin/bwa [14:49:26] Found bcftools - /usr/local/bin/bcftools [14:49:26] Found samtools - /usr/local/bin/samtools [14:49:26] Found java - /usr/local/bin/java [14:49:26] Found snpEff - /usr/local/bin/snpEff [14:49:26] Found samclip - /usr/local/bin/samclip [14:49:26] Found seqtk - /usr/local/bin/seqtk [14:49:26] Found parallel - /usr/local/bin/parallel [14:49:26] Found freebayes - /usr/local/bin/freebayes [14:49:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:49:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:49:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:49:26] Found vcfuniq - /usr/local/bin/vcfuniq [14:49:26] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:49:26] Found gzip - /bin/gzip [14:49:26] Found vt - /usr/local/bin/vt [14:49:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:49:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:49:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:49:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:49:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:49:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:49:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:49:27] Please supply a reference FASTA/GBK/EMBL file with --reference
2[14:49:11] This is snippy 4.6.0
Show full stderr[14:49:11] This is snippy 4.6.0 [14:49:11] Written by Torsten Seemann [14:49:11] Obtained from https://github.com/tseemann/snippy [14:49:11] Detected operating system: linux [14:49:11] Enabling bundled linux tools. [14:49:11] Found bwa - /usr/local/bin/bwa [14:49:11] Found bcftools - /usr/local/bin/bcftools [14:49:11] Found samtools - /usr/local/bin/samtools [14:49:11] Found java - /usr/local/bin/java [14:49:11] Found snpEff - /usr/local/bin/snpEff [14:49:11] Found samclip - /usr/local/bin/samclip [14:49:11] Found seqtk - /usr/local/bin/seqtk [14:49:11] Found parallel - /usr/local/bin/parallel [14:49:11] Found freebayes - /usr/local/bin/freebayes [14:49:11] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:49:11] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:49:11] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:49:11] Found vcfuniq - /usr/local/bin/vcfuniq [14:49:11] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:49:11] Found gzip - /bin/gzip [14:49:11] Found vt - /usr/local/bin/vt [14:49:11] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:49:11] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:49:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:49:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:49:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:49:12] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:49:12] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:49:12] Please supply a reference FASTA/GBK/EMBL file with --reference
2[14:49:40] This is snippy 4.6.0
Show full stderr[14:49:40] This is snippy 4.6.0 [14:49:40] Written by Torsten Seemann [14:49:40] Obtained from https://github.com/tseemann/snippy [14:49:40] Detected operating system: linux [14:49:40] Enabling bundled linux tools. [14:49:40] Found bwa - /usr/local/bin/bwa [14:49:40] Found bcftools - /usr/local/bin/bcftools [14:49:40] Found samtools - /usr/local/bin/samtools [14:49:40] Found java - /usr/local/bin/java [14:49:40] Found snpEff - /usr/local/bin/snpEff [14:49:40] Found samclip - /usr/local/bin/samclip [14:49:40] Found seqtk - /usr/local/bin/seqtk [14:49:40] Found parallel - /usr/local/bin/parallel [14:49:40] Found freebayes - /usr/local/bin/freebayes [14:49:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:49:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:49:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:49:40] Found vcfuniq - /usr/local/bin/vcfuniq [14:49:40] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:49:40] Found gzip - /bin/gzip [14:49:40] Found vt - /usr/local/bin/vt [14:49:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:49:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:49:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:49:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:49:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:49:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:49:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:49:41] Please supply a reference FASTA/GBK/EMBL file with --reference
2[14:49:58] This is snippy 4.6.0
Show full stderr[14:49:58] This is snippy 4.6.0 [14:49:58] Written by Torsten Seemann [14:49:58] Obtained from https://github.com/tseemann/snippy [14:49:58] Detected operating system: linux [14:49:58] Enabling bundled linux tools. [14:49:58] Found bwa - /usr/local/bin/bwa [14:49:58] Found bcftools - /usr/local/bin/bcftools [14:49:58] Found samtools - /usr/local/bin/samtools [14:49:58] Found java - /usr/local/bin/java [14:49:58] Found snpEff - /usr/local/bin/snpEff [14:49:58] Found samclip - /usr/local/bin/samclip [14:49:58] Found seqtk - /usr/local/bin/seqtk [14:49:58] Found parallel - /usr/local/bin/parallel [14:49:58] Found freebayes - /usr/local/bin/freebayes [14:49:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:49:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:49:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:49:58] Found vcfuniq - /usr/local/bin/vcfuniq [14:49:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:49:58] Found gzip - /bin/gzip [14:49:58] Found vt - /usr/local/bin/vt [14:49:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:49:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:49:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:49:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:49:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:49:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:49:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:49:59] Please supply a reference FASTA/GBK/EMBL file with --reference
2[14:51:37] This is snippy 4.6.0
Show full stderr[14:51:37] This is snippy 4.6.0 [14:51:37] Written by Torsten Seemann [14:51:37] Obtained from https://github.com/tseemann/snippy [14:51:37] Detected operating system: linux [14:51:37] Enabling bundled linux tools. [14:51:37] Found bwa - /usr/local/bin/bwa [14:51:37] Found bcftools - /usr/local/bin/bcftools [14:51:37] Found samtools - /usr/local/bin/samtools [14:51:37] Found java - /usr/local/bin/java [14:51:37] Found snpEff - /usr/local/bin/snpEff [14:51:37] Found samclip - /usr/local/bin/samclip [14:51:37] Found seqtk - /usr/local/bin/seqtk [14:51:37] Found parallel - /usr/local/bin/parallel [14:51:37] Found freebayes - /usr/local/bin/freebayes [14:51:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:51:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:51:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:51:37] Found vcfuniq - /usr/local/bin/vcfuniq [14:51:37] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:51:37] Found gzip - /bin/gzip [14:51:37] Found vt - /usr/local/bin/vt [14:51:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:51:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:51:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:51:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:51:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:51:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:51:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:51:38] Please supply a reference FASTA/GBK/EMBL file with --reference
2[14:52:23] This is snippy 4.6.0
Show full stderr[14:52:23] This is snippy 4.6.0 [14:52:23] Written by Torsten Seemann [14:52:23] Obtained from https://github.com/tseemann/snippy [14:52:23] Detected operating system: linux [14:52:23] Enabling bundled linux tools. [14:52:23] Found bwa - /usr/local/bin/bwa [14:52:23] Found bcftools - /usr/local/bin/bcftools [14:52:23] Found samtools - /usr/local/bin/samtools [14:52:23] Found java - /usr/local/bin/java [14:52:23] Found snpEff - /usr/local/bin/snpEff [14:52:23] Found samclip - /usr/local/bin/samclip [14:52:23] Found seqtk - /usr/local/bin/seqtk [14:52:23] Found parallel - /usr/local/bin/parallel [14:52:23] Found freebayes - /usr/local/bin/freebayes [14:52:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:52:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:52:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:52:23] Found vcfuniq - /usr/local/bin/vcfuniq [14:52:23] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:52:23] Found gzip - /bin/gzip [14:52:23] Found vt - /usr/local/bin/vt [14:52:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:52:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:52:23] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:52:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:52:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:52:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:52:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:52:24] Please supply a reference FASTA/GBK/EMBL file with --reference
2[14:52:35] This is snippy 4.6.0
Show full stderr[14:52:35] This is snippy 4.6.0 [14:52:35] Written by Torsten Seemann [14:52:35] Obtained from https://github.com/tseemann/snippy [14:52:35] Detected operating system: linux [14:52:35] Enabling bundled linux tools. [14:52:35] Found bwa - /usr/local/bin/bwa [14:52:35] Found bcftools - /usr/local/bin/bcftools [14:52:35] Found samtools - /usr/local/bin/samtools [14:52:35] Found java - /usr/local/bin/java [14:52:35] Found snpEff - /usr/local/bin/snpEff [14:52:35] Found samclip - /usr/local/bin/samclip [14:52:35] Found seqtk - /usr/local/bin/seqtk [14:52:35] Found parallel - /usr/local/bin/parallel [14:52:35] Found freebayes - /usr/local/bin/freebayes [14:52:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:52:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:52:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:52:35] Found vcfuniq - /usr/local/bin/vcfuniq [14:52:35] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:52:35] Found gzip - /bin/gzip [14:52:35] Found vt - /usr/local/bin/vt [14:52:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:52:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:52:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:52:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:52:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:52:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:52:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:52:35] Please supply a reference FASTA/GBK/EMBL file with --reference
2[14:50:59] This is snippy 4.6.0
Show full stderr[14:50:59] This is snippy 4.6.0 [14:50:59] Written by Torsten Seemann [14:50:59] Obtained from https://github.com/tseemann/snippy [14:50:59] Detected operating system: linux [14:50:59] Enabling bundled linux tools. [14:50:59] Found bwa - /usr/local/bin/bwa [14:50:59] Found bcftools - /usr/local/bin/bcftools [14:50:59] Found samtools - /usr/local/bin/samtools [14:50:59] Found java - /usr/local/bin/java [14:50:59] Found snpEff - /usr/local/bin/snpEff [14:50:59] Found samclip - /usr/local/bin/samclip [14:50:59] Found seqtk - /usr/local/bin/seqtk [14:50:59] Found parallel - /usr/local/bin/parallel [14:50:59] Found freebayes - /usr/local/bin/freebayes [14:50:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:50:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:51:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:51:00] Found vcfuniq - /usr/local/bin/vcfuniq [14:51:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:51:00] Found gzip - /bin/gzip [14:51:00] Found vt - /usr/local/bin/vt [14:51:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:51:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:51:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:51:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:51:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:51:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:51:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:51:00] Please supply a reference FASTA/GBK/EMBL file with --reference
2[14:51:23] This is snippy 4.6.0
Show full stderr[14:51:23] This is snippy 4.6.0 [14:51:23] Written by Torsten Seemann [14:51:23] Obtained from https://github.com/tseemann/snippy [14:51:23] Detected operating system: linux [14:51:23] Enabling bundled linux tools. [14:51:23] Found bwa - /usr/local/bin/bwa [14:51:23] Found bcftools - /usr/local/bin/bcftools [14:51:23] Found samtools - /usr/local/bin/samtools [14:51:23] Found java - /usr/local/bin/java [14:51:23] Found snpEff - /usr/local/bin/snpEff [14:51:23] Found samclip - /usr/local/bin/samclip [14:51:23] Found seqtk - /usr/local/bin/seqtk [14:51:23] Found parallel - /usr/local/bin/parallel [14:51:23] Found freebayes - /usr/local/bin/freebayes [14:51:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:51:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:51:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:51:23] Found vcfuniq - /usr/local/bin/vcfuniq [14:51:23] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:51:23] Found gzip - /bin/gzip [14:51:23] Found vt - /usr/local/bin/vt [14:51:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:51:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:51:23] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:51:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:51:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:51:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:51:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:51:23] Please supply a reference FASTA/GBK/EMBL file with --reference
2[14:52:08] This is snippy 4.6.0
Show full stderr[14:52:08] This is snippy 4.6.0 [14:52:08] Written by Torsten Seemann [14:52:08] Obtained from https://github.com/tseemann/snippy [14:52:08] Detected operating system: linux [14:52:08] Enabling bundled linux tools. [14:52:08] Found bwa - /usr/local/bin/bwa [14:52:08] Found bcftools - /usr/local/bin/bcftools [14:52:08] Found samtools - /usr/local/bin/samtools [14:52:08] Found java - /usr/local/bin/java [14:52:08] Found snpEff - /usr/local/bin/snpEff [14:52:08] Found samclip - /usr/local/bin/samclip [14:52:08] Found seqtk - /usr/local/bin/seqtk [14:52:08] Found parallel - /usr/local/bin/parallel [14:52:08] Found freebayes - /usr/local/bin/freebayes [14:52:08] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:52:08] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:52:08] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:52:08] Found vcfuniq - /usr/local/bin/vcfuniq [14:52:08] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:52:08] Found gzip - /bin/gzip [14:52:08] Found vt - /usr/local/bin/vt [14:52:08] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:52:08] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:52:08] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:52:08] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:52:08] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:52:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:52:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:52:08] Please supply a reference FASTA/GBK/EMBL file with --reference
2[14:49:44] This is snippy 4.6.0
Show full stderr[14:49:44] This is snippy 4.6.0 [14:49:44] Written by Torsten Seemann [14:49:44] Obtained from https://github.com/tseemann/snippy [14:49:44] Detected operating system: linux [14:49:44] Enabling bundled linux tools. [14:49:44] Found bwa - /usr/local/bin/bwa [14:49:44] Found bcftools - /usr/local/bin/bcftools [14:49:44] Found samtools - /usr/local/bin/samtools [14:49:44] Found java - /usr/local/bin/java [14:49:44] Found snpEff - /usr/local/bin/snpEff [14:49:44] Found samclip - /usr/local/bin/samclip [14:49:44] Found seqtk - /usr/local/bin/seqtk [14:49:44] Found parallel - /usr/local/bin/parallel [14:49:44] Found freebayes - /usr/local/bin/freebayes [14:49:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:49:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:49:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:49:44] Found vcfuniq - /usr/local/bin/vcfuniq [14:49:44] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:49:44] Found gzip - /bin/gzip [14:49:44] Found vt - /usr/local/bin/vt [14:49:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:49:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:49:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:49:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:49:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:49:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:49:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:49:44] Please supply a reference FASTA/GBK/EMBL file with --reference
2[14:51:57] This is snippy 4.6.0
Show full stderr[14:51:57] This is snippy 4.6.0 [14:51:57] Written by Torsten Seemann [14:51:57] Obtained from https://github.com/tseemann/snippy [14:51:57] Detected operating system: linux [14:51:57] Enabling bundled linux tools. [14:51:57] Found bwa - /usr/local/bin/bwa [14:51:57] Found bcftools - /usr/local/bin/bcftools [14:51:57] Found samtools - /usr/local/bin/samtools [14:51:57] Found java - /usr/local/bin/java [14:51:57] Found snpEff - /usr/local/bin/snpEff [14:51:57] Found samclip - /usr/local/bin/samclip [14:51:57] Found seqtk - /usr/local/bin/seqtk [14:51:57] Found parallel - /usr/local/bin/parallel [14:51:57] Found freebayes - /usr/local/bin/freebayes [14:51:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:51:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:51:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:51:57] Found vcfuniq - /usr/local/bin/vcfuniq [14:51:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:51:57] Found gzip - /bin/gzip [14:51:57] Found vt - /usr/local/bin/vt [14:51:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:51:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:51:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:51:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:51:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:51:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:51:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:51:58] Please supply a reference FASTA/GBK/EMBL file with --reference
2[14:53:07] This is snippy 4.6.0
Show full stderr[14:53:07] This is snippy 4.6.0 [14:53:07] Written by Torsten Seemann [14:53:07] Obtained from https://github.com/tseemann/snippy [14:53:07] Detected operating system: linux [14:53:07] Enabling bundled linux tools. [14:53:07] Found bwa - /usr/local/bin/bwa [14:53:07] Found bcftools - /usr/local/bin/bcftools [14:53:07] Found samtools - /usr/local/bin/samtools [14:53:07] Found java - /usr/local/bin/java [14:53:07] Found snpEff - /usr/local/bin/snpEff [14:53:07] Found samclip - /usr/local/bin/samclip [14:53:07] Found seqtk - /usr/local/bin/seqtk [14:53:07] Found parallel - /usr/local/bin/parallel [14:53:07] Found freebayes - /usr/local/bin/freebayes [14:53:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:53:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:53:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:53:07] Found vcfuniq - /usr/local/bin/vcfuniq [14:53:07] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:53:07] Found gzip - /bin/gzip [14:53:07] Found vt - /usr/local/bin/vt [14:53:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:53:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:53:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:53:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:53:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:53:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:53:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:53:07] Please supply a reference FASTA/GBK/EMBL file with --reference
2[14:53:19] This is snippy 4.6.0
Show full stderr[14:53:19] This is snippy 4.6.0 [14:53:19] Written by Torsten Seemann [14:53:19] Obtained from https://github.com/tseemann/snippy [14:53:19] Detected operating system: linux [14:53:19] Enabling bundled linux tools. [14:53:19] Found bwa - /usr/local/bin/bwa [14:53:19] Found bcftools - /usr/local/bin/bcftools [14:53:19] Found samtools - /usr/local/bin/samtools [14:53:19] Found java - /usr/local/bin/java [14:53:19] Found snpEff - /usr/local/bin/snpEff [14:53:19] Found samclip - /usr/local/bin/samclip [14:53:19] Found seqtk - /usr/local/bin/seqtk [14:53:19] Found parallel - /usr/local/bin/parallel [14:53:19] Found freebayes - /usr/local/bin/freebayes [14:53:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:53:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:53:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:53:19] Found vcfuniq - /usr/local/bin/vcfuniq [14:53:19] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:53:19] Found gzip - /bin/gzip [14:53:19] Found vt - /usr/local/bin/vt [14:53:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:53:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:53:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:53:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:53:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:53:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:53:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:53:20] Please supply a reference FASTA/GBK/EMBL file with --reference
2[14:53:22] This is snippy 4.6.0
Show full stderr[14:53:22] This is snippy 4.6.0 [14:53:22] Written by Torsten Seemann [14:53:22] Obtained from https://github.com/tseemann/snippy [14:53:22] Detected operating system: linux [14:53:22] Enabling bundled linux tools. [14:53:22] Found bwa - /usr/local/bin/bwa [14:53:22] Found bcftools - /usr/local/bin/bcftools [14:53:22] Found samtools - /usr/local/bin/samtools [14:53:22] Found java - /usr/local/bin/java [14:53:22] Found snpEff - /usr/local/bin/snpEff [14:53:22] Found samclip - /usr/local/bin/samclip [14:53:22] Found seqtk - /usr/local/bin/seqtk [14:53:22] Found parallel - /usr/local/bin/parallel [14:53:22] Found freebayes - /usr/local/bin/freebayes [14:53:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:53:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:53:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:53:22] Found vcfuniq - /usr/local/bin/vcfuniq [14:53:22] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:53:22] Found gzip - /bin/gzip [14:53:22] Found vt - /usr/local/bin/vt [14:53:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:53:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:53:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:53:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:53:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:53:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:53:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:53:22] Please supply a reference FASTA/GBK/EMBL file with --reference
2[14:53:33] This is snippy 4.6.0
Show full stderr[14:53:33] This is snippy 4.6.0 [14:53:33] Written by Torsten Seemann [14:53:33] Obtained from https://github.com/tseemann/snippy [14:53:33] Detected operating system: linux [14:53:33] Enabling bundled linux tools. [14:53:33] Found bwa - /usr/local/bin/bwa [14:53:33] Found bcftools - /usr/local/bin/bcftools [14:53:33] Found samtools - /usr/local/bin/samtools [14:53:33] Found java - /usr/local/bin/java [14:53:33] Found snpEff - /usr/local/bin/snpEff [14:53:33] Found samclip - /usr/local/bin/samclip [14:53:33] Found seqtk - /usr/local/bin/seqtk [14:53:33] Found parallel - /usr/local/bin/parallel [14:53:33] Found freebayes - /usr/local/bin/freebayes [14:53:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:53:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:53:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:53:33] Found vcfuniq - /usr/local/bin/vcfuniq [14:53:33] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:53:33] Found gzip - /bin/gzip [14:53:33] Found vt - /usr/local/bin/vt [14:53:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:53:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:53:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:53:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:53:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:53:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:53:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:53:34] Please supply a reference FASTA/GBK/EMBL file with --reference
2[14:53:36] This is snippy 4.6.0
Show full stderr[14:53:36] This is snippy 4.6.0 [14:53:36] Written by Torsten Seemann [14:53:36] Obtained from https://github.com/tseemann/snippy [14:53:36] Detected operating system: linux [14:53:36] Enabling bundled linux tools. [14:53:36] Found bwa - /usr/local/bin/bwa [14:53:36] Found bcftools - /usr/local/bin/bcftools [14:53:36] Found samtools - /usr/local/bin/samtools [14:53:36] Found java - /usr/local/bin/java [14:53:36] Found snpEff - /usr/local/bin/snpEff [14:53:36] Found samclip - /usr/local/bin/samclip [14:53:36] Found seqtk - /usr/local/bin/seqtk [14:53:36] Found parallel - /usr/local/bin/parallel [14:53:36] Found freebayes - /usr/local/bin/freebayes [14:53:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:53:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:53:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:53:36] Found vcfuniq - /usr/local/bin/vcfuniq [14:53:36] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:53:36] Found gzip - /bin/gzip [14:53:36] Found vt - /usr/local/bin/vt [14:53:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:53:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:53:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:53:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:53:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:53:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:53:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:53:37] Please supply a reference FASTA/GBK/EMBL file with --reference
2[14:53:47] This is snippy 4.6.0
Show full stderr[14:53:47] This is snippy 4.6.0 [14:53:47] Written by Torsten Seemann [14:53:47] Obtained from https://github.com/tseemann/snippy [14:53:47] Detected operating system: linux [14:53:47] Enabling bundled linux tools. [14:53:47] Found bwa - /usr/local/bin/bwa [14:53:47] Found bcftools - /usr/local/bin/bcftools [14:53:47] Found samtools - /usr/local/bin/samtools [14:53:47] Found java - /usr/local/bin/java [14:53:47] Found snpEff - /usr/local/bin/snpEff [14:53:47] Found samclip - /usr/local/bin/samclip [14:53:47] Found seqtk - /usr/local/bin/seqtk [14:53:47] Found parallel - /usr/local/bin/parallel [14:53:47] Found freebayes - /usr/local/bin/freebayes [14:53:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:53:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:53:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:53:47] Found vcfuniq - /usr/local/bin/vcfuniq [14:53:47] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:53:47] Found gzip - /bin/gzip [14:53:47] Found vt - /usr/local/bin/vt [14:53:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:53:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:53:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:53:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:53:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:53:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:53:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:53:48] Please supply a reference FASTA/GBK/EMBL file with --reference
2[16:04:43] This is snippy 4.6.0
Show full stderr[16:04:43] This is snippy 4.6.0 [16:04:43] Written by Torsten Seemann [16:04:43] Obtained from https://github.com/tseemann/snippy [16:04:43] Detected operating system: linux [16:04:43] Enabling bundled linux tools. [16:04:43] Found bwa - /usr/local/bin/bwa [16:04:43] Found bcftools - /usr/local/bin/bcftools [16:04:43] Found samtools - /usr/local/bin/samtools [16:04:43] Found java - /usr/local/bin/java [16:04:43] Found snpEff - /usr/local/bin/snpEff [16:04:43] Found samclip - /usr/local/bin/samclip [16:04:43] Found seqtk - /usr/local/bin/seqtk [16:04:43] Found parallel - /usr/local/bin/parallel [16:04:43] Found freebayes - /usr/local/bin/freebayes [16:04:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [16:04:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [16:04:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [16:04:43] Found vcfuniq - /usr/local/bin/vcfuniq [16:04:43] Found vcffirstheader - /usr/local/bin/vcffirstheader [16:04:43] Found gzip - /bin/gzip [16:04:43] Found vt - /usr/local/bin/vt [16:04:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [16:04:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [16:04:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [16:04:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [16:04:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [16:04:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [16:04:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [16:04:44] Please supply a reference FASTA/GBK/EMBL file with --reference
2[17:08:15] This is snippy 4.6.0
Show full stderr[17:08:15] This is snippy 4.6.0 [17:08:15] Written by Torsten Seemann [17:08:15] Obtained from https://github.com/tseemann/snippy [17:08:15] Detected operating system: linux [17:08:15] Enabling bundled linux tools. [17:08:15] Found bwa - /usr/local/bin/bwa [17:08:15] Found bcftools - /usr/local/bin/bcftools [17:08:15] Found samtools - /usr/local/bin/samtools [17:08:15] Found java - /usr/local/bin/java [17:08:15] Found snpEff - /usr/local/bin/snpEff [17:08:15] Found samclip - /usr/local/bin/samclip [17:08:15] Found seqtk - /usr/local/bin/seqtk [17:08:15] Found parallel - /usr/local/bin/parallel [17:08:15] Found freebayes - /usr/local/bin/freebayes [17:08:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:08:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:08:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:08:15] Found vcfuniq - /usr/local/bin/vcfuniq [17:08:15] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:08:15] Found gzip - /bin/gzip [17:08:15] Found vt - /usr/local/bin/vt [17:08:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:08:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:08:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:08:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:08:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:08:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:08:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:08:16] Please supply a reference FASTA/GBK/EMBL file with --reference
2[19:07:30] This is snippy 4.6.0
Show full stderr[19:07:30] This is snippy 4.6.0 [19:07:30] Written by Torsten Seemann [19:07:30] Obtained from https://github.com/tseemann/snippy [19:07:30] Detected operating system: linux [19:07:30] Enabling bundled linux tools. [19:07:30] Found bwa - /usr/local/bin/bwa [19:07:30] Found bcftools - /usr/local/bin/bcftools [19:07:30] Found samtools - /usr/local/bin/samtools [19:07:30] Found java - /usr/local/bin/java [19:07:30] Found snpEff - /usr/local/bin/snpEff [19:07:30] Found samclip - /usr/local/bin/samclip [19:07:30] Found seqtk - /usr/local/bin/seqtk [19:07:30] Found parallel - /usr/local/bin/parallel [19:07:30] Found freebayes - /usr/local/bin/freebayes [19:07:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [19:07:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [19:07:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [19:07:30] Found vcfuniq - /usr/local/bin/vcfuniq [19:07:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [19:07:30] Found gzip - /bin/gzip [19:07:30] Found vt - /usr/local/bin/vt [19:07:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [19:07:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [19:07:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [19:07:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [19:07:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [19:07:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [19:07:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [19:07:31] Please supply a reference FASTA/GBK/EMBL file with --reference
2[19:24:15] This is snippy 4.6.0
Show full stderr[19:24:15] This is snippy 4.6.0 [19:24:15] Written by Torsten Seemann [19:24:15] Obtained from https://github.com/tseemann/snippy [19:24:15] Detected operating system: linux [19:24:15] Enabling bundled linux tools. [19:24:15] Found bwa - /usr/local/bin/bwa [19:24:15] Found bcftools - /usr/local/bin/bcftools [19:24:15] Found samtools - /usr/local/bin/samtools [19:24:15] Found java - /usr/local/bin/java [19:24:15] Found snpEff - /usr/local/bin/snpEff [19:24:15] Found samclip - /usr/local/bin/samclip [19:24:15] Found seqtk - /usr/local/bin/seqtk [19:24:15] Found parallel - /usr/local/bin/parallel [19:24:15] Found freebayes - /usr/local/bin/freebayes [19:24:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [19:24:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [19:24:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [19:24:15] Found vcfuniq - /usr/local/bin/vcfuniq [19:24:15] Found vcffirstheader - /usr/local/bin/vcffirstheader [19:24:15] Found gzip - /bin/gzip [19:24:15] Found vt - /usr/local/bin/vt [19:24:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [19:24:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [19:24:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [19:24:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [19:24:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [19:24:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [19:24:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [19:24:16] Please supply a reference FASTA/GBK/EMBL file with --reference
2[17:08:31] This is snippy 4.6.0
Show full stderr[17:08:31] This is snippy 4.6.0 [17:08:31] Written by Torsten Seemann [17:08:31] Obtained from https://github.com/tseemann/snippy [17:08:31] Detected operating system: linux [17:08:31] Enabling bundled linux tools. [17:08:31] Found bwa - /usr/local/bin/bwa [17:08:31] Found bcftools - /usr/local/bin/bcftools [17:08:31] Found samtools - /usr/local/bin/samtools [17:08:31] Found java - /usr/local/bin/java [17:08:31] Found snpEff - /usr/local/bin/snpEff [17:08:31] Found samclip - /usr/local/bin/samclip [17:08:31] Found seqtk - /usr/local/bin/seqtk [17:08:31] Found parallel - /usr/local/bin/parallel [17:08:31] Found freebayes - /usr/local/bin/freebayes [17:08:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:08:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:08:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:08:31] Found vcfuniq - /usr/local/bin/vcfuniq [17:08:31] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:08:31] Found gzip - /bin/gzip [17:08:31] Found vt - /usr/local/bin/vt [17:08:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:08:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:08:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:08:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:08:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:08:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:08:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:08:32] Please supply a reference FASTA/GBK/EMBL file with --reference
2[20:14:00] This is snippy 4.6.0
Show full stderr[20:14:00] This is snippy 4.6.0 [20:14:00] Written by Torsten Seemann [20:14:00] Obtained from https://github.com/tseemann/snippy [20:14:00] Detected operating system: linux [20:14:00] Enabling bundled linux tools. [20:14:00] Found bwa - /usr/local/bin/bwa [20:14:00] Found bcftools - /usr/local/bin/bcftools [20:14:00] Found samtools - /usr/local/bin/samtools [20:14:00] Found java - /usr/local/bin/java [20:14:00] Found snpEff - /usr/local/bin/snpEff [20:14:00] Found samclip - /usr/local/bin/samclip [20:14:00] Found seqtk - /usr/local/bin/seqtk [20:14:00] Found parallel - /usr/local/bin/parallel [20:14:00] Found freebayes - /usr/local/bin/freebayes [20:14:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [20:14:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [20:14:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [20:14:00] Found vcfuniq - /usr/local/bin/vcfuniq [20:14:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [20:14:00] Found gzip - /bin/gzip [20:14:00] Found vt - /usr/local/bin/vt [20:14:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [20:14:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [20:14:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [20:14:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [20:14:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [20:14:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [20:14:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [20:14:01] Please supply a reference FASTA/GBK/EMBL file with --reference
2[18:09:47] This is snippy 4.6.0
Show full stderr[18:09:47] This is snippy 4.6.0 [18:09:47] Written by Torsten Seemann [18:09:47] Obtained from https://github.com/tseemann/snippy [18:09:47] Detected operating system: linux [18:09:47] Enabling bundled linux tools. [18:09:47] Found bwa - /usr/local/bin/bwa [18:09:47] Found bcftools - /usr/local/bin/bcftools [18:09:47] Found samtools - /usr/local/bin/samtools [18:09:47] Found java - /usr/local/bin/java [18:09:47] Found snpEff - /usr/local/bin/snpEff [18:09:47] Found samclip - /usr/local/bin/samclip [18:09:47] Found seqtk - /usr/local/bin/seqtk [18:09:47] Found parallel - /usr/local/bin/parallel [18:09:47] Found freebayes - /usr/local/bin/freebayes [18:09:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [18:09:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [18:09:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [18:09:47] Found vcfuniq - /usr/local/bin/vcfuniq [18:09:47] Found vcffirstheader - /usr/local/bin/vcffirstheader [18:09:47] Found gzip - /bin/gzip [18:09:47] Found vt - /usr/local/bin/vt [18:09:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [18:09:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [18:09:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [18:09:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [18:09:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [18:09:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [18:09:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [18:09:48] Please supply a reference FASTA/GBK/EMBL file with --reference
2[17:25:46] This is snippy 4.6.0
Show full stderr[17:25:46] This is snippy 4.6.0 [17:25:46] Written by Torsten Seemann [17:25:46] Obtained from https://github.com/tseemann/snippy [17:25:46] Detected operating system: linux [17:25:46] Enabling bundled linux tools. [17:25:46] Found bwa - /usr/local/bin/bwa [17:25:46] Found bcftools - /usr/local/bin/bcftools [17:25:46] Found samtools - /usr/local/bin/samtools [17:25:46] Found java - /usr/local/bin/java [17:25:46] Found snpEff - /usr/local/bin/snpEff [17:25:46] Found samclip - /usr/local/bin/samclip [17:25:46] Found seqtk - /usr/local/bin/seqtk [17:25:46] Found parallel - /usr/local/bin/parallel [17:25:46] Found freebayes - /usr/local/bin/freebayes [17:25:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:25:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:25:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:25:46] Found vcfuniq - /usr/local/bin/vcfuniq [17:25:46] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:25:46] Found gzip - /bin/gzip [17:25:46] Found vt - /usr/local/bin/vt [17:25:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:25:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:25:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:25:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:25:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:25:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:25:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:25:47] Please supply a reference FASTA/GBK/EMBL file with --reference
2[17:25:31] This is snippy 4.6.0
Show full stderr[17:25:31] This is snippy 4.6.0 [17:25:31] Written by Torsten Seemann [17:25:31] Obtained from https://github.com/tseemann/snippy [17:25:31] Detected operating system: linux [17:25:31] Enabling bundled linux tools. [17:25:31] Found bwa - /usr/local/bin/bwa [17:25:31] Found bcftools - /usr/local/bin/bcftools [17:25:31] Found samtools - /usr/local/bin/samtools [17:25:31] Found java - /usr/local/bin/java [17:25:31] Found snpEff - /usr/local/bin/snpEff [17:25:31] Found samclip - /usr/local/bin/samclip [17:25:31] Found seqtk - /usr/local/bin/seqtk [17:25:31] Found parallel - /usr/local/bin/parallel [17:25:31] Found freebayes - /usr/local/bin/freebayes [17:25:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:25:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:25:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:25:31] Found vcfuniq - /usr/local/bin/vcfuniq [17:25:31] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:25:31] Found gzip - /bin/gzip [17:25:31] Found vt - /usr/local/bin/vt [17:25:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:25:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:25:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:25:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:25:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:25:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:25:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:25:32] Please supply a reference FASTA/GBK/EMBL file with --reference
2[20:47:17] This is snippy 4.6.0
Show full stderr[20:47:17] This is snippy 4.6.0 [20:47:17] Written by Torsten Seemann [20:47:17] Obtained from https://github.com/tseemann/snippy [20:47:17] Detected operating system: linux [20:47:17] Enabling bundled linux tools. [20:47:17] Found bwa - /usr/local/bin/bwa [20:47:17] Found bcftools - /usr/local/bin/bcftools [20:47:17] Found samtools - /usr/local/bin/samtools [20:47:17] Found java - /usr/local/bin/java [20:47:17] Found snpEff - /usr/local/bin/snpEff [20:47:17] Found samclip - /usr/local/bin/samclip [20:47:17] Found seqtk - /usr/local/bin/seqtk [20:47:17] Found parallel - /usr/local/bin/parallel [20:47:17] Found freebayes - /usr/local/bin/freebayes [20:47:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [20:47:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [20:47:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [20:47:17] Found vcfuniq - /usr/local/bin/vcfuniq [20:47:17] Found vcffirstheader - /usr/local/bin/vcffirstheader [20:47:17] Found gzip - /bin/gzip [20:47:17] Found vt - /usr/local/bin/vt [20:47:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [20:47:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [20:47:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [20:47:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [20:47:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [20:47:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [20:47:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [20:47:18] Please supply a reference FASTA/GBK/EMBL file with --reference
2[16:12:47] This is snippy 4.6.0
Show full stderr[16:12:47] This is snippy 4.6.0 [16:12:47] Written by Torsten Seemann [16:12:47] Obtained from https://github.com/tseemann/snippy [16:12:47] Detected operating system: linux [16:12:47] Enabling bundled linux tools. [16:12:47] Found bwa - /usr/local/bin/bwa [16:12:47] Found bcftools - /usr/local/bin/bcftools [16:12:47] Found samtools - /usr/local/bin/samtools [16:12:47] Found java - /usr/local/bin/java [16:12:47] Found snpEff - /usr/local/bin/snpEff [16:12:47] Found samclip - /usr/local/bin/samclip [16:12:47] Found seqtk - /usr/local/bin/seqtk [16:12:47] Found parallel - /usr/local/bin/parallel [16:12:47] Found freebayes - /usr/local/bin/freebayes [16:12:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [16:12:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [16:12:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [16:12:47] Found vcfuniq - /usr/local/bin/vcfuniq [16:12:47] Found vcffirstheader - /usr/local/bin/vcffirstheader [16:12:47] Found gzip - /bin/gzip [16:12:47] Found vt - /usr/local/bin/vt [16:12:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [16:12:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [16:12:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [16:12:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [16:12:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [16:12:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [16:12:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [16:12:48] Please supply a reference FASTA/GBK/EMBL file with --reference
2[21:21:09] This is snippy 4.6.0
Show full stderr[21:21:09] This is snippy 4.6.0 [21:21:09] Written by Torsten Seemann [21:21:09] Obtained from https://github.com/tseemann/snippy [21:21:09] Detected operating system: linux [21:21:09] Enabling bundled linux tools. [21:21:09] Found bwa - /usr/local/bin/bwa [21:21:09] Found bcftools - /usr/local/bin/bcftools [21:21:09] Found samtools - /usr/local/bin/samtools [21:21:09] Found java - /usr/local/bin/java [21:21:09] Found snpEff - /usr/local/bin/snpEff [21:21:09] Found samclip - /usr/local/bin/samclip [21:21:09] Found seqtk - /usr/local/bin/seqtk [21:21:09] Found parallel - /usr/local/bin/parallel [21:21:09] Found freebayes - /usr/local/bin/freebayes [21:21:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:21:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:21:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:21:09] Found vcfuniq - /usr/local/bin/vcfuniq [21:21:09] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:21:09] Found gzip - /bin/gzip [21:21:09] Found vt - /usr/local/bin/vt [21:21:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:21:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:21:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:21:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:21:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:21:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:21:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:21:10] Please supply a reference FASTA/GBK/EMBL file with --reference
2[00:43:50] This is snippy 4.6.0
Show full stderr[00:43:50] This is snippy 4.6.0 [00:43:50] Written by Torsten Seemann [00:43:50] Obtained from https://github.com/tseemann/snippy [00:43:50] Detected operating system: linux [00:43:50] Enabling bundled linux tools. [00:43:50] Found bwa - /usr/local/bin/bwa [00:43:50] Found bcftools - /usr/local/bin/bcftools [00:43:50] Found samtools - /usr/local/bin/samtools [00:43:50] Found java - /usr/local/bin/java [00:43:50] Found snpEff - /usr/local/bin/snpEff [00:43:50] Found samclip - /usr/local/bin/samclip [00:43:50] Found seqtk - /usr/local/bin/seqtk [00:43:50] Found parallel - /usr/local/bin/parallel [00:43:50] Found freebayes - /usr/local/bin/freebayes [00:43:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:43:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:43:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:43:50] Found vcfuniq - /usr/local/bin/vcfuniq [00:43:50] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:43:50] Found gzip - /bin/gzip [00:43:50] Found vt - /usr/local/bin/vt [00:43:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:43:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:43:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:43:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:43:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:43:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:43:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:43:51] Please supply a reference FASTA/GBK/EMBL file with --reference
2[00:24:45] This is snippy 4.6.0
Show full stderr[00:24:45] This is snippy 4.6.0 [00:24:45] Written by Torsten Seemann [00:24:45] Obtained from https://github.com/tseemann/snippy [00:24:45] Detected operating system: linux [00:24:45] Enabling bundled linux tools. [00:24:45] Found bwa - /usr/local/bin/bwa [00:24:45] Found bcftools - /usr/local/bin/bcftools [00:24:45] Found samtools - /usr/local/bin/samtools [00:24:45] Found java - /usr/local/bin/java [00:24:45] Found snpEff - /usr/local/bin/snpEff [00:24:45] Found samclip - /usr/local/bin/samclip [00:24:45] Found seqtk - /usr/local/bin/seqtk [00:24:45] Found parallel - /usr/local/bin/parallel [00:24:45] Found freebayes - /usr/local/bin/freebayes [00:24:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:24:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:24:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:24:45] Found vcfuniq - /usr/local/bin/vcfuniq [00:24:45] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:24:45] Found gzip - /bin/gzip [00:24:45] Found vt - /usr/local/bin/vt [00:24:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:24:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:24:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:24:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:24:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:24:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:24:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:24:46] Please supply a reference FASTA/GBK/EMBL file with --reference
2[09:34:49] This is snippy 4.6.0
Show full stderr[09:34:49] This is snippy 4.6.0 [09:34:49] Written by Torsten Seemann [09:34:49] Obtained from https://github.com/tseemann/snippy [09:34:49] Detected operating system: linux [09:34:49] Enabling bundled linux tools. [09:34:49] Found bwa - /usr/local/bin/bwa [09:34:49] Found bcftools - /usr/local/bin/bcftools [09:34:49] Found samtools - /usr/local/bin/samtools [09:34:49] Found java - /usr/local/bin/java [09:34:49] Found snpEff - /usr/local/bin/snpEff [09:34:49] Found samclip - /usr/local/bin/samclip [09:34:49] Found seqtk - /usr/local/bin/seqtk [09:34:49] Found parallel - /usr/local/bin/parallel [09:34:49] Found freebayes - /usr/local/bin/freebayes [09:34:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [09:34:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [09:34:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [09:34:49] Found vcfuniq - /usr/local/bin/vcfuniq [09:34:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [09:34:49] Found gzip - /bin/gzip [09:34:49] Found vt - /usr/local/bin/vt [09:34:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [09:34:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [09:34:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [09:34:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [09:34:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [09:34:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [09:34:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [09:34:52] Using reference: /jetstream2/scratch/main/jobs/72478615/inputs/dataset_d3c82029-edc2-407d-bfbf-3c19136e7bbb.dat [09:34:52] Treating reference as 'fasta' format. [09:34:52] Will use 1 CPU cores. [09:34:52] Using read file: /jetstream2/scratch/main/jobs/72478615/inputs/dataset_1dddc894-0e35-4e4b-b92d-42c90d918535.dat [09:34:52] Using read file: /jetstream2/scratch/main/jobs/72478615/inputs/dataset_1dddc894-0e35-4e4b-b92d-42c90d918535.dat [09:34:52] Creating folder: SCA4_21 [09:34:52] Changing working directory: SCA4_21 [09:34:52] Creating reference folder: reference [09:34:52] Extracting FASTA and GFF from reference. [09:34:53] Wrote 3 sequences to ref.fa [09:34:53] Wrote 0 features to ref.gff [09:34:53] Freebayes will process 1 chunks of 9205924 bp, 1 chunks at a time. [09:34:53] Using BAM RG (Read Group) ID: SCA4_21 [09:34:53] Running: samtools faidx reference/ref.fa 2>> snps.log [09:34:53] Running: bwa index reference/ref.fa 2>> snps.log [09:34:56] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [09:34:56] Running: ln -sf reference/ref.fa . 2>> snps.log [09:34:56] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [09:34:56] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [09:34:56] Running: bwa mem -Y -M -R '@RG\tID:SCA4_21\tSM:SCA4_21' -t 1 reference/ref.fa /jetstream2/scratch/main/jobs/72478615/inputs/dataset_1dddc894-0e35-4e4b-b92d-42c90d918535.dat /jetstream2/scratch/main/jobs/72478615/inputs/dataset_1dddc894-0e35-4e4b-b92d-42c90d918535.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/72478615/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/72478615/tmp --threads 0 -m 12000M | samtools markdup -T /jetstream2/scratch/main/jobs/72478615/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: refere
2[17:23:48] This is snippy 4.6.0
Show full stderr[17:23:48] This is snippy 4.6.0 [17:23:48] Written by Torsten Seemann [17:23:48] Obtained from https://github.com/tseemann/snippy [17:23:48] Detected operating system: linux [17:23:48] Enabling bundled linux tools. [17:23:48] Found bwa - /usr/local/bin/bwa [17:23:48] Found bcftools - /usr/local/bin/bcftools [17:23:48] Found samtools - /usr/local/bin/samtools [17:23:48] Found java - /usr/local/bin/java [17:23:48] Found snpEff - /usr/local/bin/snpEff [17:23:48] Found samclip - /usr/local/bin/samclip [17:23:48] Found seqtk - /usr/local/bin/seqtk [17:23:48] Found parallel - /usr/local/bin/parallel [17:23:48] Found freebayes - /usr/local/bin/freebayes [17:23:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:23:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:23:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:23:48] Found vcfuniq - /usr/local/bin/vcfuniq [17:23:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:23:48] Found gzip - /bin/gzip [17:23:48] Found vt - /usr/local/bin/vt [17:23:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:23:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:23:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:23:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:23:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:23:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:23:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:23:49] Please supply a reference FASTA/GBK/EMBL file with --reference
2[17:24:27] This is snippy 4.6.0
Show full stderr[17:24:27] This is snippy 4.6.0 [17:24:27] Written by Torsten Seemann [17:24:27] Obtained from https://github.com/tseemann/snippy [17:24:27] Detected operating system: linux [17:24:27] Enabling bundled linux tools. [17:24:27] Found bwa - /usr/local/bin/bwa [17:24:27] Found bcftools - /usr/local/bin/bcftools [17:24:27] Found samtools - /usr/local/bin/samtools [17:24:27] Found java - /usr/local/bin/java [17:24:27] Found snpEff - /usr/local/bin/snpEff [17:24:27] Found samclip - /usr/local/bin/samclip [17:24:27] Found seqtk - /usr/local/bin/seqtk [17:24:27] Found parallel - /usr/local/bin/parallel [17:24:27] Found freebayes - /usr/local/bin/freebayes [17:24:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:24:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:24:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:24:27] Found vcfuniq - /usr/local/bin/vcfuniq [17:24:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:24:27] Found gzip - /bin/gzip [17:24:27] Found vt - /usr/local/bin/vt [17:24:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:24:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:24:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:24:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:24:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:24:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:24:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:24:28] Please supply a reference FASTA/GBK/EMBL file with --reference
2[17:27:28] This is snippy 4.6.0
Show full stderr[17:27:28] This is snippy 4.6.0 [17:27:28] Written by Torsten Seemann [17:27:28] Obtained from https://github.com/tseemann/snippy [17:27:28] Detected operating system: linux [17:27:28] Enabling bundled linux tools. [17:27:28] Found bwa - /usr/local/bin/bwa [17:27:28] Found bcftools - /usr/local/bin/bcftools [17:27:28] Found samtools - /usr/local/bin/samtools [17:27:28] Found java - /usr/local/bin/java [17:27:28] Found snpEff - /usr/local/bin/snpEff [17:27:28] Found samclip - /usr/local/bin/samclip [17:27:28] Found seqtk - /usr/local/bin/seqtk [17:27:28] Found parallel - /usr/local/bin/parallel [17:27:28] Found freebayes - /usr/local/bin/freebayes [17:27:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:27:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:27:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:27:28] Found vcfuniq - /usr/local/bin/vcfuniq [17:27:28] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:27:28] Found gzip - /bin/gzip [17:27:28] Found vt - /usr/local/bin/vt [17:27:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:27:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:27:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:27:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:27:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:27:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:27:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:27:29] Please supply a reference FASTA/GBK/EMBL file with --reference
2[17:49:04] This is snippy 4.6.0
Show full stderr[17:49:04] This is snippy 4.6.0 [17:49:04] Written by Torsten Seemann [17:49:04] Obtained from https://github.com/tseemann/snippy [17:49:04] Detected operating system: linux [17:49:04] Enabling bundled linux tools. [17:49:04] Found bwa - /usr/local/bin/bwa [17:49:04] Found bcftools - /usr/local/bin/bcftools [17:49:04] Found samtools - /usr/local/bin/samtools [17:49:04] Found java - /usr/local/bin/java [17:49:04] Found snpEff - /usr/local/bin/snpEff [17:49:04] Found samclip - /usr/local/bin/samclip [17:49:04] Found seqtk - /usr/local/bin/seqtk [17:49:04] Found parallel - /usr/local/bin/parallel [17:49:04] Found freebayes - /usr/local/bin/freebayes [17:49:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:49:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:49:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:49:04] Found vcfuniq - /usr/local/bin/vcfuniq [17:49:04] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:49:04] Found gzip - /bin/gzip [17:49:04] Found vt - /usr/local/bin/vt [17:49:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:49:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:49:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:49:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:49:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:49:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:49:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:49:04] Please supply a reference FASTA/GBK/EMBL file with --reference
2[17:23:51] This is snippy 4.6.0
Show full stderr[17:23:51] This is snippy 4.6.0 [17:23:51] Written by Torsten Seemann [17:23:51] Obtained from https://github.com/tseemann/snippy [17:23:51] Detected operating system: linux [17:23:51] Enabling bundled linux tools. [17:23:51] Found bwa - /usr/local/bin/bwa [17:23:51] Found bcftools - /usr/local/bin/bcftools [17:23:51] Found samtools - /usr/local/bin/samtools [17:23:51] Found java - /usr/local/bin/java [17:23:51] Found snpEff - /usr/local/bin/snpEff [17:23:51] Found samclip - /usr/local/bin/samclip [17:23:51] Found seqtk - /usr/local/bin/seqtk [17:23:51] Found parallel - /usr/local/bin/parallel [17:23:51] Found freebayes - /usr/local/bin/freebayes [17:23:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:23:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:23:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:23:51] Found vcfuniq - /usr/local/bin/vcfuniq [17:23:51] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:23:51] Found gzip - /bin/gzip [17:23:51] Found vt - /usr/local/bin/vt [17:23:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:23:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:23:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:23:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:23:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:23:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:23:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:23:52] Please supply a reference FASTA/GBK/EMBL file with --reference
2[17:23:59] This is snippy 4.6.0
Show full stderr[17:23:59] This is snippy 4.6.0 [17:23:59] Written by Torsten Seemann [17:23:59] Obtained from https://github.com/tseemann/snippy [17:23:59] Detected operating system: linux [17:23:59] Enabling bundled linux tools. [17:23:59] Found bwa - /usr/local/bin/bwa [17:23:59] Found bcftools - /usr/local/bin/bcftools [17:23:59] Found samtools - /usr/local/bin/samtools [17:23:59] Found java - /usr/local/bin/java [17:23:59] Found snpEff - /usr/local/bin/snpEff [17:23:59] Found samclip - /usr/local/bin/samclip [17:23:59] Found seqtk - /usr/local/bin/seqtk [17:23:59] Found parallel - /usr/local/bin/parallel [17:23:59] Found freebayes - /usr/local/bin/freebayes [17:23:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:23:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:23:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:23:59] Found vcfuniq - /usr/local/bin/vcfuniq [17:23:59] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:23:59] Found gzip - /bin/gzip [17:23:59] Found vt - /usr/local/bin/vt [17:23:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:23:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:24:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:24:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:24:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:24:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:24:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:24:06] Please supply a reference FASTA/GBK/EMBL file with --reference
2[17:25:21] This is snippy 4.6.0
Show full stderr[17:25:21] This is snippy 4.6.0 [17:25:21] Written by Torsten Seemann [17:25:21] Obtained from https://github.com/tseemann/snippy [17:25:21] Detected operating system: linux [17:25:21] Enabling bundled linux tools. [17:25:21] Found bwa - /usr/local/bin/bwa [17:25:21] Found bcftools - /usr/local/bin/bcftools [17:25:21] Found samtools - /usr/local/bin/samtools [17:25:21] Found java - /usr/local/bin/java [17:25:21] Found snpEff - /usr/local/bin/snpEff [17:25:21] Found samclip - /usr/local/bin/samclip [17:25:21] Found seqtk - /usr/local/bin/seqtk [17:25:21] Found parallel - /usr/local/bin/parallel [17:25:21] Found freebayes - /usr/local/bin/freebayes [17:25:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:25:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:25:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:25:21] Found vcfuniq - /usr/local/bin/vcfuniq [17:25:21] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:25:21] Found gzip - /bin/gzip [17:25:21] Found vt - /usr/local/bin/vt [17:25:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:25:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:25:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:25:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:25:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:25:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:25:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:25:22] Please supply a reference FASTA/GBK/EMBL file with --reference
2[17:29:17] This is snippy 4.6.0
Show full stderr[17:29:17] This is snippy 4.6.0 [17:29:17] Written by Torsten Seemann [17:29:17] Obtained from https://github.com/tseemann/snippy [17:29:17] Detected operating system: linux [17:29:17] Enabling bundled linux tools. [17:29:17] Found bwa - /usr/local/bin/bwa [17:29:17] Found bcftools - /usr/local/bin/bcftools [17:29:17] Found samtools - /usr/local/bin/samtools [17:29:17] Found java - /usr/local/bin/java [17:29:17] Found snpEff - /usr/local/bin/snpEff [17:29:17] Found samclip - /usr/local/bin/samclip [17:29:17] Found seqtk - /usr/local/bin/seqtk [17:29:17] Found parallel - /usr/local/bin/parallel [17:29:17] Found freebayes - /usr/local/bin/freebayes [17:29:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:29:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:29:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:29:17] Found vcfuniq - /usr/local/bin/vcfuniq [17:29:17] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:29:17] Found gzip - /bin/gzip [17:29:17] Found vt - /usr/local/bin/vt [17:29:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:29:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:29:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:29:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:29:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:29:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:29:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:29:18] Please supply a reference FASTA/GBK/EMBL file with --reference
2[17:29:36] This is snippy 4.6.0
Show full stderr[17:29:36] This is snippy 4.6.0 [17:29:36] Written by Torsten Seemann [17:29:36] Obtained from https://github.com/tseemann/snippy [17:29:36] Detected operating system: linux [17:29:36] Enabling bundled linux tools. [17:29:36] Found bwa - /usr/local/bin/bwa [17:29:36] Found bcftools - /usr/local/bin/bcftools [17:29:36] Found samtools - /usr/local/bin/samtools [17:29:36] Found java - /usr/local/bin/java [17:29:36] Found snpEff - /usr/local/bin/snpEff [17:29:36] Found samclip - /usr/local/bin/samclip [17:29:36] Found seqtk - /usr/local/bin/seqtk [17:29:36] Found parallel - /usr/local/bin/parallel [17:29:36] Found freebayes - /usr/local/bin/freebayes [17:29:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:29:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:29:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:29:36] Found vcfuniq - /usr/local/bin/vcfuniq [17:29:36] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:29:36] Found gzip - /bin/gzip [17:29:36] Found vt - /usr/local/bin/vt [17:29:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:29:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:29:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:29:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:29:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:29:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:29:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:29:37] Please supply a reference FASTA/GBK/EMBL file with --reference
2[17:30:23] This is snippy 4.6.0
Show full stderr[17:30:23] This is snippy 4.6.0 [17:30:23] Written by Torsten Seemann [17:30:23] Obtained from https://github.com/tseemann/snippy [17:30:23] Detected operating system: linux [17:30:23] Enabling bundled linux tools. [17:30:23] Found bwa - /usr/local/bin/bwa [17:30:23] Found bcftools - /usr/local/bin/bcftools [17:30:23] Found samtools - /usr/local/bin/samtools [17:30:23] Found java - /usr/local/bin/java [17:30:23] Found snpEff - /usr/local/bin/snpEff [17:30:23] Found samclip - /usr/local/bin/samclip [17:30:23] Found seqtk - /usr/local/bin/seqtk [17:30:23] Found parallel - /usr/local/bin/parallel [17:30:23] Found freebayes - /usr/local/bin/freebayes [17:30:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:30:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:30:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:30:23] Found vcfuniq - /usr/local/bin/vcfuniq [17:30:23] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:30:23] Found gzip - /bin/gzip [17:30:23] Found vt - /usr/local/bin/vt [17:30:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:30:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:30:23] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:30:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:30:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:30:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:30:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:30:24] Please supply a reference FASTA/GBK/EMBL file with --reference
2[17:39:54] This is snippy 4.6.0
Show full stderr[17:39:54] This is snippy 4.6.0 [17:39:54] Written by Torsten Seemann [17:39:54] Obtained from https://github.com/tseemann/snippy [17:39:54] Detected operating system: linux [17:39:54] Enabling bundled linux tools. [17:39:54] Found bwa - /usr/local/bin/bwa [17:39:54] Found bcftools - /usr/local/bin/bcftools [17:39:54] Found samtools - /usr/local/bin/samtools [17:39:54] Found java - /usr/local/bin/java [17:39:54] Found snpEff - /usr/local/bin/snpEff [17:39:54] Found samclip - /usr/local/bin/samclip [17:39:54] Found seqtk - /usr/local/bin/seqtk [17:39:54] Found parallel - /usr/local/bin/parallel [17:39:54] Found freebayes - /usr/local/bin/freebayes [17:39:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:39:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:39:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:39:54] Found vcfuniq - /usr/local/bin/vcfuniq [17:39:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:39:54] Found gzip - /bin/gzip [17:39:54] Found vt - /usr/local/bin/vt [17:39:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:39:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:39:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:39:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:39:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:39:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:39:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:39:55] Please supply a reference FASTA/GBK/EMBL file with --reference
2[17:41:06] This is snippy 4.6.0
Show full stderr[17:41:06] This is snippy 4.6.0 [17:41:06] Written by Torsten Seemann [17:41:06] Obtained from https://github.com/tseemann/snippy [17:41:06] Detected operating system: linux [17:41:06] Enabling bundled linux tools. [17:41:06] Found bwa - /usr/local/bin/bwa [17:41:06] Found bcftools - /usr/local/bin/bcftools [17:41:06] Found samtools - /usr/local/bin/samtools [17:41:06] Found java - /usr/local/bin/java [17:41:06] Found snpEff - /usr/local/bin/snpEff [17:41:06] Found samclip - /usr/local/bin/samclip [17:41:06] Found seqtk - /usr/local/bin/seqtk [17:41:07] Found parallel - /usr/local/bin/parallel [17:41:07] Found freebayes - /usr/local/bin/freebayes [17:41:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:41:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:41:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:41:07] Found vcfuniq - /usr/local/bin/vcfuniq [17:41:07] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:41:07] Found gzip - /bin/gzip [17:41:07] Found vt - /usr/local/bin/vt [17:41:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:41:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:41:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:41:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:41:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:41:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:41:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:41:08] Please supply a reference FASTA/GBK/EMBL file with --reference
2[17:41:34] This is snippy 4.6.0
Show full stderr[17:41:34] This is snippy 4.6.0 [17:41:34] Written by Torsten Seemann [17:41:34] Obtained from https://github.com/tseemann/snippy [17:41:34] Detected operating system: linux [17:41:34] Enabling bundled linux tools. [17:41:34] Found bwa - /usr/local/bin/bwa [17:41:34] Found bcftools - /usr/local/bin/bcftools [17:41:34] Found samtools - /usr/local/bin/samtools [17:41:34] Found java - /usr/local/bin/java [17:41:34] Found snpEff - /usr/local/bin/snpEff [17:41:34] Found samclip - /usr/local/bin/samclip [17:41:34] Found seqtk - /usr/local/bin/seqtk [17:41:34] Found parallel - /usr/local/bin/parallel [17:41:34] Found freebayes - /usr/local/bin/freebayes [17:41:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:41:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:41:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:41:34] Found vcfuniq - /usr/local/bin/vcfuniq [17:41:34] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:41:34] Found gzip - /bin/gzip [17:41:34] Found vt - /usr/local/bin/vt [17:41:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:41:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:41:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:41:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:41:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:41:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:41:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:41:35] Please supply a reference FASTA/GBK/EMBL file with --reference
2[17:38:54] This is snippy 4.6.0
Show full stderr[17:38:54] This is snippy 4.6.0 [17:38:54] Written by Torsten Seemann [17:38:54] Obtained from https://github.com/tseemann/snippy [17:38:54] Detected operating system: linux [17:38:54] Enabling bundled linux tools. [17:38:54] Found bwa - /usr/local/bin/bwa [17:38:54] Found bcftools - /usr/local/bin/bcftools [17:38:54] Found samtools - /usr/local/bin/samtools [17:38:54] Found java - /usr/local/bin/java [17:38:54] Found snpEff - /usr/local/bin/snpEff [17:38:54] Found samclip - /usr/local/bin/samclip [17:38:55] Found seqtk - /usr/local/bin/seqtk [17:38:55] Found parallel - /usr/local/bin/parallel [17:38:55] Found freebayes - /usr/local/bin/freebayes [17:38:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:38:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:38:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:38:55] Found vcfuniq - /usr/local/bin/vcfuniq [17:38:55] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:38:55] Found gzip - /bin/gzip [17:38:55] Found vt - /usr/local/bin/vt [17:38:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:38:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:38:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:38:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:38:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:38:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:38:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:38:56] Please supply a reference FASTA/GBK/EMBL file with --reference
2[17:41:21] This is snippy 4.6.0
Show full stderr[17:41:21] This is snippy 4.6.0 [17:41:21] Written by Torsten Seemann [17:41:21] Obtained from https://github.com/tseemann/snippy [17:41:21] Detected operating system: linux [17:41:21] Enabling bundled linux tools. [17:41:21] Found bwa - /usr/local/bin/bwa [17:41:21] Found bcftools - /usr/local/bin/bcftools [17:41:21] Found samtools - /usr/local/bin/samtools [17:41:21] Found java - /usr/local/bin/java [17:41:21] Found snpEff - /usr/local/bin/snpEff [17:41:22] Found samclip - /usr/local/bin/samclip [17:41:22] Found seqtk - /usr/local/bin/seqtk [17:41:22] Found parallel - /usr/local/bin/parallel [17:41:22] Found freebayes - /usr/local/bin/freebayes [17:41:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:41:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:41:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:41:22] Found vcfuniq - /usr/local/bin/vcfuniq [17:41:22] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:41:22] Found gzip - /bin/gzip [17:41:22] Found vt - /usr/local/bin/vt [17:41:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:41:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:41:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:41:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:41:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:41:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:41:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:41:23] Please supply a reference FASTA/GBK/EMBL file with --reference
2[17:42:45] This is snippy 4.6.0
Show full stderr[17:42:45] This is snippy 4.6.0 [17:42:45] Written by Torsten Seemann [17:42:45] Obtained from https://github.com/tseemann/snippy [17:42:45] Detected operating system: linux [17:42:45] Enabling bundled linux tools. [17:42:45] Found bwa - /usr/local/bin/bwa [17:42:45] Found bcftools - /usr/local/bin/bcftools [17:42:45] Found samtools - /usr/local/bin/samtools [17:42:45] Found java - /usr/local/bin/java [17:42:45] Found snpEff - /usr/local/bin/snpEff [17:42:45] Found samclip - /usr/local/bin/samclip [17:42:45] Found seqtk - /usr/local/bin/seqtk [17:42:45] Found parallel - /usr/local/bin/parallel [17:42:45] Found freebayes - /usr/local/bin/freebayes [17:42:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:42:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:42:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:42:45] Found vcfuniq - /usr/local/bin/vcfuniq [17:42:45] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:42:45] Found gzip - /bin/gzip [17:42:45] Found vt - /usr/local/bin/vt [17:42:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:42:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:42:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:42:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:42:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:42:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:42:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:42:46] Please supply a reference FASTA/GBK/EMBL file with --reference
2[17:44:58] This is snippy 4.6.0
Show full stderr[17:44:58] This is snippy 4.6.0 [17:44:58] Written by Torsten Seemann [17:44:58] Obtained from https://github.com/tseemann/snippy [17:44:58] Detected operating system: linux [17:44:58] Enabling bundled linux tools. [17:44:58] Found bwa - /usr/local/bin/bwa [17:44:58] Found bcftools - /usr/local/bin/bcftools [17:44:58] Found samtools - /usr/local/bin/samtools [17:44:58] Found java - /usr/local/bin/java [17:44:58] Found snpEff - /usr/local/bin/snpEff [17:44:58] Found samclip - /usr/local/bin/samclip [17:44:58] Found seqtk - /usr/local/bin/seqtk [17:44:58] Found parallel - /usr/local/bin/parallel [17:44:59] Found freebayes - /usr/local/bin/freebayes [17:44:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:44:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:44:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:44:59] Found vcfuniq - /usr/local/bin/vcfuniq [17:44:59] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:44:59] Found gzip - /bin/gzip [17:44:59] Found vt - /usr/local/bin/vt [17:44:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:44:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:44:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:44:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:44:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:45:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:45:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:45:00] Please supply a reference FASTA/GBK/EMBL file with --reference
2[17:40:45] This is snippy 4.6.0
Show full stderr[17:40:45] This is snippy 4.6.0 [17:40:45] Written by Torsten Seemann [17:40:45] Obtained from https://github.com/tseemann/snippy [17:40:45] Detected operating system: linux [17:40:45] Enabling bundled linux tools. [17:40:45] Found bwa - /usr/local/bin/bwa [17:40:45] Found bcftools - /usr/local/bin/bcftools [17:40:45] Found samtools - /usr/local/bin/samtools [17:40:45] Found java - /usr/local/bin/java [17:40:45] Found snpEff - /usr/local/bin/snpEff [17:40:45] Found samclip - /usr/local/bin/samclip [17:40:45] Found seqtk - /usr/local/bin/seqtk [17:40:45] Found parallel - /usr/local/bin/parallel [17:40:45] Found freebayes - /usr/local/bin/freebayes [17:40:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:40:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:40:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:40:45] Found vcfuniq - /usr/local/bin/vcfuniq [17:40:45] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:40:45] Found gzip - /bin/gzip [17:40:45] Found vt - /usr/local/bin/vt [17:40:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:40:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:40:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:40:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:40:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:40:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:40:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:40:47] Please supply a reference FASTA/GBK/EMBL file with --reference
2[17:37:54] This is snippy 4.6.0
Show full stderr[17:37:54] This is snippy 4.6.0 [17:37:54] Written by Torsten Seemann [17:37:54] Obtained from https://github.com/tseemann/snippy [17:37:54] Detected operating system: linux [17:37:54] Enabling bundled linux tools. [17:37:54] Found bwa - /usr/local/bin/bwa [17:37:54] Found bcftools - /usr/local/bin/bcftools [17:37:54] Found samtools - /usr/local/bin/samtools [17:37:54] Found java - /usr/local/bin/java [17:37:54] Found snpEff - /usr/local/bin/snpEff [17:37:54] Found samclip - /usr/local/bin/samclip [17:37:54] Found seqtk - /usr/local/bin/seqtk [17:37:54] Found parallel - /usr/local/bin/parallel [17:37:54] Found freebayes - /usr/local/bin/freebayes [17:37:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:37:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:37:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:37:54] Found vcfuniq - /usr/local/bin/vcfuniq [17:37:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:37:54] Found gzip - /bin/gzip [17:37:54] Found vt - /usr/local/bin/vt [17:37:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:37:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:37:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:37:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:37:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:37:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:37:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:37:54] Please supply a reference FASTA/GBK/EMBL file with --reference
2[17:43:38] This is snippy 4.6.0
Show full stderr[17:43:38] This is snippy 4.6.0 [17:43:38] Written by Torsten Seemann [17:43:38] Obtained from https://github.com/tseemann/snippy [17:43:38] Detected operating system: linux [17:43:38] Enabling bundled linux tools. [17:43:38] Found bwa - /usr/local/bin/bwa [17:43:38] Found bcftools - /usr/local/bin/bcftools [17:43:38] Found samtools - /usr/local/bin/samtools [17:43:38] Found java - /usr/local/bin/java [17:43:38] Found snpEff - /usr/local/bin/snpEff [17:43:38] Found samclip - /usr/local/bin/samclip [17:43:38] Found seqtk - /usr/local/bin/seqtk [17:43:38] Found parallel - /usr/local/bin/parallel [17:43:38] Found freebayes - /usr/local/bin/freebayes [17:43:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:43:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:43:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:43:39] Found vcfuniq - /usr/local/bin/vcfuniq [17:43:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:43:39] Found gzip - /bin/gzip [17:43:39] Found vt - /usr/local/bin/vt [17:43:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:43:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:43:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:43:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:43:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:43:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:43:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:43:40] Please supply a reference FASTA/GBK/EMBL file with --reference
2[17:48:46] This is snippy 4.6.0
Show full stderr[17:48:46] This is snippy 4.6.0 [17:48:46] Written by Torsten Seemann [17:48:46] Obtained from https://github.com/tseemann/snippy [17:48:46] Detected operating system: linux [17:48:46] Enabling bundled linux tools. [17:48:46] Found bwa - /usr/local/bin/bwa [17:48:46] Found bcftools - /usr/local/bin/bcftools [17:48:46] Found samtools - /usr/local/bin/samtools [17:48:46] Found java - /usr/local/bin/java [17:48:46] Found snpEff - /usr/local/bin/snpEff [17:48:46] Found samclip - /usr/local/bin/samclip [17:48:46] Found seqtk - /usr/local/bin/seqtk [17:48:46] Found parallel - /usr/local/bin/parallel [17:48:46] Found freebayes - /usr/local/bin/freebayes [17:48:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:48:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:48:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:48:46] Found vcfuniq - /usr/local/bin/vcfuniq [17:48:46] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:48:46] Found gzip - /bin/gzip [17:48:46] Found vt - /usr/local/bin/vt [17:48:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:48:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:48:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:48:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:48:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:48:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:48:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:48:49] Please supply a reference FASTA/GBK/EMBL file with --reference
2[00:23:35] This is snippy 4.6.0
Show full stderr[00:23:35] This is snippy 4.6.0 [00:23:35] Written by Torsten Seemann [00:23:35] Obtained from https://github.com/tseemann/snippy [00:23:35] Detected operating system: linux [00:23:35] Enabling bundled linux tools. [00:23:35] Found bwa - /usr/local/bin/bwa [00:23:35] Found bcftools - /usr/local/bin/bcftools [00:23:35] Found samtools - /usr/local/bin/samtools [00:23:35] Found java - /usr/local/bin/java [00:23:35] Found snpEff - /usr/local/bin/snpEff [00:23:35] Found samclip - /usr/local/bin/samclip [00:23:35] Found seqtk - /usr/local/bin/seqtk [00:23:35] Found parallel - /usr/local/bin/parallel [00:23:35] Found freebayes - /usr/local/bin/freebayes [00:23:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:23:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:23:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:23:35] Found vcfuniq - /usr/local/bin/vcfuniq [00:23:35] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:23:35] Found gzip - /bin/gzip [00:23:35] Found vt - /usr/local/bin/vt [00:23:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:23:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:23:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:23:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:23:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:23:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:23:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:23:36] Please supply a reference FASTA/GBK/EMBL file with --reference
2[00:23:45] This is snippy 4.6.0
Show full stderr[00:23:45] This is snippy 4.6.0 [00:23:45] Written by Torsten Seemann [00:23:45] Obtained from https://github.com/tseemann/snippy [00:23:45] Detected operating system: linux [00:23:45] Enabling bundled linux tools. [00:23:45] Found bwa - /usr/local/bin/bwa [00:23:45] Found bcftools - /usr/local/bin/bcftools [00:23:45] Found samtools - /usr/local/bin/samtools [00:23:45] Found java - /usr/local/bin/java [00:23:45] Found snpEff - /usr/local/bin/snpEff [00:23:45] Found samclip - /usr/local/bin/samclip [00:23:45] Found seqtk - /usr/local/bin/seqtk [00:23:45] Found parallel - /usr/local/bin/parallel [00:23:45] Found freebayes - /usr/local/bin/freebayes [00:23:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:23:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:23:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:23:45] Found vcfuniq - /usr/local/bin/vcfuniq [00:23:45] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:23:45] Found gzip - /bin/gzip [00:23:45] Found vt - /usr/local/bin/vt [00:23:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:23:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:23:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:23:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:23:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:23:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:23:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:23:46] Please supply a reference FASTA/GBK/EMBL file with --reference
2[00:23:57] This is snippy 4.6.0
Show full stderr[00:23:57] This is snippy 4.6.0 [00:23:57] Written by Torsten Seemann [00:23:57] Obtained from https://github.com/tseemann/snippy [00:23:57] Detected operating system: linux [00:23:57] Enabling bundled linux tools. [00:23:57] Found bwa - /usr/local/bin/bwa [00:23:57] Found bcftools - /usr/local/bin/bcftools [00:23:57] Found samtools - /usr/local/bin/samtools [00:23:57] Found java - /usr/local/bin/java [00:23:57] Found snpEff - /usr/local/bin/snpEff [00:23:57] Found samclip - /usr/local/bin/samclip [00:23:57] Found seqtk - /usr/local/bin/seqtk [00:23:57] Found parallel - /usr/local/bin/parallel [00:23:57] Found freebayes - /usr/local/bin/freebayes [00:23:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:23:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:23:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:23:57] Found vcfuniq - /usr/local/bin/vcfuniq [00:23:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:23:57] Found gzip - /bin/gzip [00:23:57] Found vt - /usr/local/bin/vt [00:23:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:23:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:23:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:23:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:23:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:23:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:23:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:23:58] Please supply a reference FASTA/GBK/EMBL file with --reference
2[00:24:00] This is snippy 4.6.0
Show full stderr[00:24:00] This is snippy 4.6.0 [00:24:00] Written by Torsten Seemann [00:24:00] Obtained from https://github.com/tseemann/snippy [00:24:00] Detected operating system: linux [00:24:00] Enabling bundled linux tools. [00:24:00] Found bwa - /usr/local/bin/bwa [00:24:00] Found bcftools - /usr/local/bin/bcftools [00:24:00] Found samtools - /usr/local/bin/samtools [00:24:00] Found java - /usr/local/bin/java [00:24:00] Found snpEff - /usr/local/bin/snpEff [00:24:00] Found samclip - /usr/local/bin/samclip [00:24:00] Found seqtk - /usr/local/bin/seqtk [00:24:00] Found parallel - /usr/local/bin/parallel [00:24:00] Found freebayes - /usr/local/bin/freebayes [00:24:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:24:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:24:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:24:00] Found vcfuniq - /usr/local/bin/vcfuniq [00:24:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:24:00] Found gzip - /bin/gzip [00:24:00] Found vt - /usr/local/bin/vt [00:24:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:24:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:24:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:24:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:24:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:24:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:24:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:24:01] Please supply a reference FASTA/GBK/EMBL file with --reference
2[00:24:12] This is snippy 4.6.0
Show full stderr[00:24:12] This is snippy 4.6.0 [00:24:12] Written by Torsten Seemann [00:24:12] Obtained from https://github.com/tseemann/snippy [00:24:12] Detected operating system: linux [00:24:12] Enabling bundled linux tools. [00:24:12] Found bwa - /usr/local/bin/bwa [00:24:12] Found bcftools - /usr/local/bin/bcftools [00:24:12] Found samtools - /usr/local/bin/samtools [00:24:12] Found java - /usr/local/bin/java [00:24:12] Found snpEff - /usr/local/bin/snpEff [00:24:12] Found samclip - /usr/local/bin/samclip [00:24:12] Found seqtk - /usr/local/bin/seqtk [00:24:12] Found parallel - /usr/local/bin/parallel [00:24:12] Found freebayes - /usr/local/bin/freebayes [00:24:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:24:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:24:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:24:12] Found vcfuniq - /usr/local/bin/vcfuniq [00:24:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:24:12] Found gzip - /bin/gzip [00:24:12] Found vt - /usr/local/bin/vt [00:24:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:24:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:24:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:24:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:24:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:24:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:24:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:24:13] Please supply a reference FASTA/GBK/EMBL file with --reference
2[00:24:15] This is snippy 4.6.0
Show full stderr[00:24:15] This is snippy 4.6.0 [00:24:15] Written by Torsten Seemann [00:24:15] Obtained from https://github.com/tseemann/snippy [00:24:15] Detected operating system: linux [00:24:15] Enabling bundled linux tools. [00:24:15] Found bwa - /usr/local/bin/bwa [00:24:15] Found bcftools - /usr/local/bin/bcftools [00:24:15] Found samtools - /usr/local/bin/samtools [00:24:15] Found java - /usr/local/bin/java [00:24:15] Found snpEff - /usr/local/bin/snpEff [00:24:15] Found samclip - /usr/local/bin/samclip [00:24:15] Found seqtk - /usr/local/bin/seqtk [00:24:15] Found parallel - /usr/local/bin/parallel [00:24:15] Found freebayes - /usr/local/bin/freebayes [00:24:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:24:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:24:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:24:15] Found vcfuniq - /usr/local/bin/vcfuniq [00:24:15] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:24:15] Found gzip - /bin/gzip [00:24:15] Found vt - /usr/local/bin/vt [00:24:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:24:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:24:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:24:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:24:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:24:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:24:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:24:16] Please supply a reference FASTA/GBK/EMBL file with --reference
2[00:24:43] This is snippy 4.6.0
Show full stderr[00:24:43] This is snippy 4.6.0 [00:24:43] Written by Torsten Seemann [00:24:43] Obtained from https://github.com/tseemann/snippy [00:24:43] Detected operating system: linux [00:24:43] Enabling bundled linux tools. [00:24:43] Found bwa - /usr/local/bin/bwa [00:24:43] Found bcftools - /usr/local/bin/bcftools [00:24:43] Found samtools - /usr/local/bin/samtools [00:24:43] Found java - /usr/local/bin/java [00:24:43] Found snpEff - /usr/local/bin/snpEff [00:24:43] Found samclip - /usr/local/bin/samclip [00:24:43] Found seqtk - /usr/local/bin/seqtk [00:24:43] Found parallel - /usr/local/bin/parallel [00:24:43] Found freebayes - /usr/local/bin/freebayes [00:24:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:24:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:24:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:24:43] Found vcfuniq - /usr/local/bin/vcfuniq [00:24:43] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:24:43] Found gzip - /bin/gzip [00:24:43] Found vt - /usr/local/bin/vt [00:24:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:24:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:24:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:24:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:24:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:24:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:24:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:24:45] Please supply a reference FASTA/GBK/EMBL file with --reference
2[00:25:33] This is snippy 4.6.0
Show full stderr[00:25:33] This is snippy 4.6.0 [00:25:33] Written by Torsten Seemann [00:25:33] Obtained from https://github.com/tseemann/snippy [00:25:33] Detected operating system: linux [00:25:33] Enabling bundled linux tools. [00:25:33] Found bwa - /usr/local/bin/bwa [00:25:33] Found bcftools - /usr/local/bin/bcftools [00:25:33] Found samtools - /usr/local/bin/samtools [00:25:33] Found java - /usr/local/bin/java [00:25:33] Found snpEff - /usr/local/bin/snpEff [00:25:33] Found samclip - /usr/local/bin/samclip [00:25:33] Found seqtk - /usr/local/bin/seqtk [00:25:33] Found parallel - /usr/local/bin/parallel [00:25:33] Found freebayes - /usr/local/bin/freebayes [00:25:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:25:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:25:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:25:33] Found vcfuniq - /usr/local/bin/vcfuniq [00:25:33] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:25:33] Found gzip - /bin/gzip [00:25:33] Found vt - /usr/local/bin/vt [00:25:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:25:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:25:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:25:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:25:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:25:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:25:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:25:35] Please supply a reference FASTA/GBK/EMBL file with --reference
2[00:26:21] This is snippy 4.6.0
Show full stderr[00:26:21] This is snippy 4.6.0 [00:26:21] Written by Torsten Seemann [00:26:21] Obtained from https://github.com/tseemann/snippy [00:26:21] Detected operating system: linux [00:26:21] Enabling bundled linux tools. [00:26:21] Found bwa - /usr/local/bin/bwa [00:26:21] Found bcftools - /usr/local/bin/bcftools [00:26:21] Found samtools - /usr/local/bin/samtools [00:26:21] Found java - /usr/local/bin/java [00:26:21] Found snpEff - /usr/local/bin/snpEff [00:26:21] Found samclip - /usr/local/bin/samclip [00:26:21] Found seqtk - /usr/local/bin/seqtk [00:26:21] Found parallel - /usr/local/bin/parallel [00:26:21] Found freebayes - /usr/local/bin/freebayes [00:26:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:26:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:26:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:26:21] Found vcfuniq - /usr/local/bin/vcfuniq [00:26:21] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:26:21] Found gzip - /bin/gzip [00:26:21] Found vt - /usr/local/bin/vt [00:26:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:26:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:26:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:26:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:26:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:26:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:26:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:26:22] Please supply a reference FASTA/GBK/EMBL file with --reference
2[00:26:48] This is snippy 4.6.0
Show full stderr[00:26:48] This is snippy 4.6.0 [00:26:48] Written by Torsten Seemann [00:26:48] Obtained from https://github.com/tseemann/snippy [00:26:48] Detected operating system: linux [00:26:48] Enabling bundled linux tools. [00:26:48] Found bwa - /usr/local/bin/bwa [00:26:48] Found bcftools - /usr/local/bin/bcftools [00:26:48] Found samtools - /usr/local/bin/samtools [00:26:48] Found java - /usr/local/bin/java [00:26:48] Found snpEff - /usr/local/bin/snpEff [00:26:48] Found samclip - /usr/local/bin/samclip [00:26:48] Found seqtk - /usr/local/bin/seqtk [00:26:48] Found parallel - /usr/local/bin/parallel [00:26:48] Found freebayes - /usr/local/bin/freebayes [00:26:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:26:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:26:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:26:48] Found vcfuniq - /usr/local/bin/vcfuniq [00:26:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:26:48] Found gzip - /bin/gzip [00:26:48] Found vt - /usr/local/bin/vt [00:26:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:26:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:26:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:26:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:26:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:26:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:26:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:26:49] Please supply a reference FASTA/GBK/EMBL file with --reference
2[00:27:27] This is snippy 4.6.0
Show full stderr[00:27:27] This is snippy 4.6.0 [00:27:27] Written by Torsten Seemann [00:27:27] Obtained from https://github.com/tseemann/snippy [00:27:27] Detected operating system: linux [00:27:27] Enabling bundled linux tools. [00:27:27] Found bwa - /usr/local/bin/bwa [00:27:27] Found bcftools - /usr/local/bin/bcftools [00:27:27] Found samtools - /usr/local/bin/samtools [00:27:27] Found java - /usr/local/bin/java [00:27:27] Found snpEff - /usr/local/bin/snpEff [00:27:27] Found samclip - /usr/local/bin/samclip [00:27:27] Found seqtk - /usr/local/bin/seqtk [00:27:27] Found parallel - /usr/local/bin/parallel [00:27:27] Found freebayes - /usr/local/bin/freebayes [00:27:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:27:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:27:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:27:27] Found vcfuniq - /usr/local/bin/vcfuniq [00:27:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:27:27] Found gzip - /bin/gzip [00:27:27] Found vt - /usr/local/bin/vt [00:27:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:27:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:27:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:27:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:27:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:27:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:27:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:27:28] Please supply a reference FASTA/GBK/EMBL file with --reference
2[00:27:21] This is snippy 4.6.0
Show full stderr[00:27:21] This is snippy 4.6.0 [00:27:21] Written by Torsten Seemann [00:27:21] Obtained from https://github.com/tseemann/snippy [00:27:21] Detected operating system: linux [00:27:21] Enabling bundled linux tools. [00:27:21] Found bwa - /usr/local/bin/bwa [00:27:21] Found bcftools - /usr/local/bin/bcftools [00:27:21] Found samtools - /usr/local/bin/samtools [00:27:21] Found java - /usr/local/bin/java [00:27:21] Found snpEff - /usr/local/bin/snpEff [00:27:21] Found samclip - /usr/local/bin/samclip [00:27:21] Found seqtk - /usr/local/bin/seqtk [00:27:21] Found parallel - /usr/local/bin/parallel [00:27:21] Found freebayes - /usr/local/bin/freebayes [00:27:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:27:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:27:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:27:21] Found vcfuniq - /usr/local/bin/vcfuniq [00:27:21] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:27:21] Found gzip - /bin/gzip [00:27:21] Found vt - /usr/local/bin/vt [00:27:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:27:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:27:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:27:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:27:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:27:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:27:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:27:22] Please supply a reference FASTA/GBK/EMBL file with --reference
2[00:29:57] This is snippy 4.6.0
Show full stderr[00:29:57] This is snippy 4.6.0 [00:29:57] Written by Torsten Seemann [00:29:57] Obtained from https://github.com/tseemann/snippy [00:29:57] Detected operating system: linux [00:29:57] Enabling bundled linux tools. [00:29:57] Found bwa - /usr/local/bin/bwa [00:29:57] Found bcftools - /usr/local/bin/bcftools [00:29:57] Found samtools - /usr/local/bin/samtools [00:29:57] Found java - /usr/local/bin/java [00:29:57] Found snpEff - /usr/local/bin/snpEff [00:29:57] Found samclip - /usr/local/bin/samclip [00:29:57] Found seqtk - /usr/local/bin/seqtk [00:29:57] Found parallel - /usr/local/bin/parallel [00:29:57] Found freebayes - /usr/local/bin/freebayes [00:29:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:29:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:29:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:29:57] Found vcfuniq - /usr/local/bin/vcfuniq [00:29:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:29:57] Found gzip - /bin/gzip [00:29:57] Found vt - /usr/local/bin/vt [00:29:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:29:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:29:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:29:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:29:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:29:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:29:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:29:58] Please supply a reference FASTA/GBK/EMBL file with --reference
2[00:42:17] This is snippy 4.6.0
Show full stderr[00:42:17] This is snippy 4.6.0 [00:42:17] Written by Torsten Seemann [00:42:17] Obtained from https://github.com/tseemann/snippy [00:42:17] Detected operating system: linux [00:42:17] Enabling bundled linux tools. [00:42:17] Found bwa - /usr/local/bin/bwa [00:42:17] Found bcftools - /usr/local/bin/bcftools [00:42:17] Found samtools - /usr/local/bin/samtools [00:42:17] Found java - /usr/local/bin/java [00:42:17] Found snpEff - /usr/local/bin/snpEff [00:42:17] Found samclip - /usr/local/bin/samclip [00:42:17] Found seqtk - /usr/local/bin/seqtk [00:42:17] Found parallel - /usr/local/bin/parallel [00:42:17] Found freebayes - /usr/local/bin/freebayes [00:42:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:42:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:42:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:42:18] Found vcfuniq - /usr/local/bin/vcfuniq [00:42:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:42:18] Found gzip - /bin/gzip [00:42:18] Found vt - /usr/local/bin/vt [00:42:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:42:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:42:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:42:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:42:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:42:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:42:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:42:23] Please supply a reference FASTA/GBK/EMBL file with --reference
2[00:32:51] This is snippy 4.6.0
Show full stderr[00:32:51] This is snippy 4.6.0 [00:32:51] Written by Torsten Seemann [00:32:51] Obtained from https://github.com/tseemann/snippy [00:32:51] Detected operating system: linux [00:32:51] Enabling bundled linux tools. [00:32:51] Found bwa - /usr/local/bin/bwa [00:32:51] Found bcftools - /usr/local/bin/bcftools [00:32:51] Found samtools - /usr/local/bin/samtools [00:32:51] Found java - /usr/local/bin/java [00:32:51] Found snpEff - /usr/local/bin/snpEff [00:32:51] Found samclip - /usr/local/bin/samclip [00:32:51] Found seqtk - /usr/local/bin/seqtk [00:32:51] Found parallel - /usr/local/bin/parallel [00:32:51] Found freebayes - /usr/local/bin/freebayes [00:32:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:32:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:32:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:32:51] Found vcfuniq - /usr/local/bin/vcfuniq [00:32:51] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:32:51] Found gzip - /bin/gzip [00:32:51] Found vt - /usr/local/bin/vt [00:32:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:32:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:32:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:32:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:32:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:32:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:32:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:32:52] Please supply a reference FASTA/GBK/EMBL file with --reference
2[00:29:54] This is snippy 4.6.0
Show full stderr[00:29:54] This is snippy 4.6.0 [00:29:54] Written by Torsten Seemann [00:29:54] Obtained from https://github.com/tseemann/snippy [00:29:54] Detected operating system: linux [00:29:54] Enabling bundled linux tools. [00:29:54] Found bwa - /usr/local/bin/bwa [00:29:54] Found bcftools - /usr/local/bin/bcftools [00:29:54] Found samtools - /usr/local/bin/samtools [00:29:54] Found java - /usr/local/bin/java [00:29:54] Found snpEff - /usr/local/bin/snpEff [00:29:54] Found samclip - /usr/local/bin/samclip [00:29:54] Found seqtk - /usr/local/bin/seqtk [00:29:54] Found parallel - /usr/local/bin/parallel [00:29:54] Found freebayes - /usr/local/bin/freebayes [00:29:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:29:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:29:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:29:54] Found vcfuniq - /usr/local/bin/vcfuniq [00:29:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:29:54] Found gzip - /bin/gzip [00:29:54] Found vt - /usr/local/bin/vt [00:29:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:29:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:29:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:29:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:29:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:29:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:29:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:29:54] Please supply a reference FASTA/GBK/EMBL file with --reference
2[00:30:09] This is snippy 4.6.0
Show full stderr[00:30:09] This is snippy 4.6.0 [00:30:09] Written by Torsten Seemann [00:30:09] Obtained from https://github.com/tseemann/snippy [00:30:09] Detected operating system: linux [00:30:09] Enabling bundled linux tools. [00:30:09] Found bwa - /usr/local/bin/bwa [00:30:09] Found bcftools - /usr/local/bin/bcftools [00:30:09] Found samtools - /usr/local/bin/samtools [00:30:09] Found java - /usr/local/bin/java [00:30:09] Found snpEff - /usr/local/bin/snpEff [00:30:09] Found samclip - /usr/local/bin/samclip [00:30:09] Found seqtk - /usr/local/bin/seqtk [00:30:09] Found parallel - /usr/local/bin/parallel [00:30:09] Found freebayes - /usr/local/bin/freebayes [00:30:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:30:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:30:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:30:09] Found vcfuniq - /usr/local/bin/vcfuniq [00:30:09] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:30:09] Found gzip - /bin/gzip [00:30:09] Found vt - /usr/local/bin/vt [00:30:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:30:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:30:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:30:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:30:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:30:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:30:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:30:10] Please supply a reference FASTA/GBK/EMBL file with --reference
2[00:31:33] This is snippy 4.6.0
Show full stderr[00:31:33] This is snippy 4.6.0 [00:31:33] Written by Torsten Seemann [00:31:33] Obtained from https://github.com/tseemann/snippy [00:31:33] Detected operating system: linux [00:31:33] Enabling bundled linux tools. [00:31:33] Found bwa - /usr/local/bin/bwa [00:31:33] Found bcftools - /usr/local/bin/bcftools [00:31:33] Found samtools - /usr/local/bin/samtools [00:31:33] Found java - /usr/local/bin/java [00:31:33] Found snpEff - /usr/local/bin/snpEff [00:31:33] Found samclip - /usr/local/bin/samclip [00:31:33] Found seqtk - /usr/local/bin/seqtk [00:31:33] Found parallel - /usr/local/bin/parallel [00:31:33] Found freebayes - /usr/local/bin/freebayes [00:31:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:31:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:31:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:31:33] Found vcfuniq - /usr/local/bin/vcfuniq [00:31:33] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:31:33] Found gzip - /bin/gzip [00:31:33] Found vt - /usr/local/bin/vt [00:31:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:31:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:31:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:31:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:31:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:31:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:31:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:31:34] Please supply a reference FASTA/GBK/EMBL file with --reference
2[00:28:31] This is snippy 4.6.0
Show full stderr[00:28:31] This is snippy 4.6.0 [00:28:31] Written by Torsten Seemann [00:28:31] Obtained from https://github.com/tseemann/snippy [00:28:31] Detected operating system: linux [00:28:31] Enabling bundled linux tools. [00:28:31] Found bwa - /usr/local/bin/bwa [00:28:31] Found bcftools - /usr/local/bin/bcftools [00:28:31] Found samtools - /usr/local/bin/samtools [00:28:31] Found java - /usr/local/bin/java [00:28:31] Found snpEff - /usr/local/bin/snpEff [00:28:31] Found samclip - /usr/local/bin/samclip [00:28:31] Found seqtk - /usr/local/bin/seqtk [00:28:31] Found parallel - /usr/local/bin/parallel [00:28:31] Found freebayes - /usr/local/bin/freebayes [00:28:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:28:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:28:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:28:31] Found vcfuniq - /usr/local/bin/vcfuniq [00:28:31] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:28:31] Found gzip - /bin/gzip [00:28:31] Found vt - /usr/local/bin/vt [00:28:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:28:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:28:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:28:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:28:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:28:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:28:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:28:32] Please supply a reference FASTA/GBK/EMBL file with --reference
2[00:29:20] This is snippy 4.6.0
Show full stderr[00:29:20] This is snippy 4.6.0 [00:29:20] Written by Torsten Seemann [00:29:20] Obtained from https://github.com/tseemann/snippy [00:29:20] Detected operating system: linux [00:29:20] Enabling bundled linux tools. [00:29:20] Found bwa - /usr/local/bin/bwa [00:29:21] Found bcftools - /usr/local/bin/bcftools [00:29:21] Found samtools - /usr/local/bin/samtools [00:29:21] Found java - /usr/local/bin/java [00:29:21] Found snpEff - /usr/local/bin/snpEff [00:29:21] Found samclip - /usr/local/bin/samclip [00:29:21] Found seqtk - /usr/local/bin/seqtk [00:29:21] Found parallel - /usr/local/bin/parallel [00:29:21] Found freebayes - /usr/local/bin/freebayes [00:29:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:29:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:29:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:29:21] Found vcfuniq - /usr/local/bin/vcfuniq [00:29:21] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:29:21] Found gzip - /bin/gzip [00:29:21] Found vt - /usr/local/bin/vt [00:29:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:29:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:29:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:29:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:29:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:29:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:29:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:29:21] Please supply a reference FASTA/GBK/EMBL file with --reference
2[00:32:04] This is snippy 4.6.0
Show full stderr[00:32:04] This is snippy 4.6.0 [00:32:04] Written by Torsten Seemann [00:32:04] Obtained from https://github.com/tseemann/snippy [00:32:04] Detected operating system: linux [00:32:04] Enabling bundled linux tools. [00:32:04] Found bwa - /usr/local/bin/bwa [00:32:04] Found bcftools - /usr/local/bin/bcftools [00:32:04] Found samtools - /usr/local/bin/samtools [00:32:04] Found java - /usr/local/bin/java [00:32:04] Found snpEff - /usr/local/bin/snpEff [00:32:04] Found samclip - /usr/local/bin/samclip [00:32:04] Found seqtk - /usr/local/bin/seqtk [00:32:04] Found parallel - /usr/local/bin/parallel [00:32:04] Found freebayes - /usr/local/bin/freebayes [00:32:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:32:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:32:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:32:04] Found vcfuniq - /usr/local/bin/vcfuniq [00:32:04] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:32:04] Found gzip - /bin/gzip [00:32:04] Found vt - /usr/local/bin/vt [00:32:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:32:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:32:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:32:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:32:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:32:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:32:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:32:05] Please supply a reference FASTA/GBK/EMBL file with --reference
2[01:23:37] This is snippy 4.6.0
Show full stderr[01:23:37] This is snippy 4.6.0 [01:23:37] Written by Torsten Seemann [01:23:37] Obtained from https://github.com/tseemann/snippy [01:23:37] Detected operating system: linux [01:23:37] Enabling bundled linux tools. [01:23:37] Found bwa - /usr/local/bin/bwa [01:23:37] Found bcftools - /usr/local/bin/bcftools [01:23:37] Found samtools - /usr/local/bin/samtools [01:23:37] Found java - /usr/local/bin/java [01:23:37] Found snpEff - /usr/local/bin/snpEff [01:23:37] Found samclip - /usr/local/bin/samclip [01:23:37] Found seqtk - /usr/local/bin/seqtk [01:23:37] Found parallel - /usr/local/bin/parallel [01:23:37] Found freebayes - /usr/local/bin/freebayes [01:23:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:23:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:23:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:23:37] Found vcfuniq - /usr/local/bin/vcfuniq [01:23:37] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:23:37] Found gzip - /bin/gzip [01:23:37] Found vt - /usr/local/bin/vt [01:23:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:23:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:23:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:23:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:23:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:23:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:23:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:23:38] Please supply a reference FASTA/GBK/EMBL file with --reference
2[00:32:37] This is snippy 4.6.0
Show full stderr[00:32:37] This is snippy 4.6.0 [00:32:37] Written by Torsten Seemann [00:32:37] Obtained from https://github.com/tseemann/snippy [00:32:37] Detected operating system: linux [00:32:37] Enabling bundled linux tools. [00:32:37] Found bwa - /usr/local/bin/bwa [00:32:37] Found bcftools - /usr/local/bin/bcftools [00:32:37] Found samtools - /usr/local/bin/samtools [00:32:37] Found java - /usr/local/bin/java [00:32:37] Found snpEff - /usr/local/bin/snpEff [00:32:37] Found samclip - /usr/local/bin/samclip [00:32:37] Found seqtk - /usr/local/bin/seqtk [00:32:37] Found parallel - /usr/local/bin/parallel [00:32:37] Found freebayes - /usr/local/bin/freebayes [00:32:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:32:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:32:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:32:37] Found vcfuniq - /usr/local/bin/vcfuniq [00:32:37] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:32:37] Found gzip - /bin/gzip [00:32:37] Found vt - /usr/local/bin/vt [00:32:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:32:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:32:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:32:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:32:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:32:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:32:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:32:38] Please supply a reference FASTA/GBK/EMBL file with --reference
2[00:34:39] This is snippy 4.6.0
Show full stderr[00:34:39] This is snippy 4.6.0 [00:34:39] Written by Torsten Seemann [00:34:39] Obtained from https://github.com/tseemann/snippy [00:34:39] Detected operating system: linux [00:34:39] Enabling bundled linux tools. [00:34:39] Found bwa - /usr/local/bin/bwa [00:34:39] Found bcftools - /usr/local/bin/bcftools [00:34:39] Found samtools - /usr/local/bin/samtools [00:34:39] Found java - /usr/local/bin/java [00:34:39] Found snpEff - /usr/local/bin/snpEff [00:34:39] Found samclip - /usr/local/bin/samclip [00:34:39] Found seqtk - /usr/local/bin/seqtk [00:34:39] Found parallel - /usr/local/bin/parallel [00:34:39] Found freebayes - /usr/local/bin/freebayes [00:34:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:34:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:34:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:34:39] Found vcfuniq - /usr/local/bin/vcfuniq [00:34:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:34:39] Found gzip - /bin/gzip [00:34:39] Found vt - /usr/local/bin/vt [00:34:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:34:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:34:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:34:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:34:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:34:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:34:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:34:40] Please supply a reference FASTA/GBK/EMBL file with --reference
2[00:44:19] This is snippy 4.6.0
Show full stderr[00:44:19] This is snippy 4.6.0 [00:44:19] Written by Torsten Seemann [00:44:19] Obtained from https://github.com/tseemann/snippy [00:44:19] Detected operating system: linux [00:44:19] Enabling bundled linux tools. [00:44:19] Found bwa - /usr/local/bin/bwa [00:44:19] Found bcftools - /usr/local/bin/bcftools [00:44:19] Found samtools - /usr/local/bin/samtools [00:44:19] Found java - /usr/local/bin/java [00:44:19] Found snpEff - /usr/local/bin/snpEff [00:44:19] Found samclip - /usr/local/bin/samclip [00:44:19] Found seqtk - /usr/local/bin/seqtk [00:44:19] Found parallel - /usr/local/bin/parallel [00:44:19] Found freebayes - /usr/local/bin/freebayes [00:44:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:44:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:44:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:44:19] Found vcfuniq - /usr/local/bin/vcfuniq [00:44:19] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:44:19] Found gzip - /bin/gzip [00:44:19] Found vt - /usr/local/bin/vt [00:44:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:44:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:44:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:44:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:44:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:44:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:44:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:44:20] Please supply a reference FASTA/GBK/EMBL file with --reference
2[00:33:42] This is snippy 4.6.0
Show full stderr[00:33:42] This is snippy 4.6.0 [00:33:42] Written by Torsten Seemann [00:33:42] Obtained from https://github.com/tseemann/snippy [00:33:42] Detected operating system: linux [00:33:42] Enabling bundled linux tools. [00:33:42] Found bwa - /usr/local/bin/bwa [00:33:42] Found bcftools - /usr/local/bin/bcftools [00:33:42] Found samtools - /usr/local/bin/samtools [00:33:42] Found java - /usr/local/bin/java [00:33:42] Found snpEff - /usr/local/bin/snpEff [00:33:42] Found samclip - /usr/local/bin/samclip [00:33:42] Found seqtk - /usr/local/bin/seqtk [00:33:42] Found parallel - /usr/local/bin/parallel [00:33:42] Found freebayes - /usr/local/bin/freebayes [00:33:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:33:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:33:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:33:42] Found vcfuniq - /usr/local/bin/vcfuniq [00:33:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:33:42] Found gzip - /bin/gzip [00:33:42] Found vt - /usr/local/bin/vt [00:33:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:33:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:33:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:33:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:33:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:33:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:33:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:33:43] Please supply a reference FASTA/GBK/EMBL file with --reference
2[00:48:20] This is snippy 4.6.0
Show full stderr[00:48:20] This is snippy 4.6.0 [00:48:20] Written by Torsten Seemann [00:48:20] Obtained from https://github.com/tseemann/snippy [00:48:20] Detected operating system: linux [00:48:20] Enabling bundled linux tools. [00:48:20] Found bwa - /usr/local/bin/bwa [00:48:20] Found bcftools - /usr/local/bin/bcftools [00:48:20] Found samtools - /usr/local/bin/samtools [00:48:20] Found java - /usr/local/bin/java [00:48:20] Found snpEff - /usr/local/bin/snpEff [00:48:20] Found samclip - /usr/local/bin/samclip [00:48:20] Found seqtk - /usr/local/bin/seqtk [00:48:20] Found parallel - /usr/local/bin/parallel [00:48:20] Found freebayes - /usr/local/bin/freebayes [00:48:20] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:48:20] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:48:20] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:48:20] Found vcfuniq - /usr/local/bin/vcfuniq [00:48:20] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:48:20] Found gzip - /bin/gzip [00:48:20] Found vt - /usr/local/bin/vt [00:48:20] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:48:20] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:48:20] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:48:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:48:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:48:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:48:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:48:21] Please supply a reference FASTA/GBK/EMBL file with --reference
2[00:34:03] This is snippy 4.6.0
Show full stderr[00:34:03] This is snippy 4.6.0 [00:34:03] Written by Torsten Seemann [00:34:03] Obtained from https://github.com/tseemann/snippy [00:34:03] Detected operating system: linux [00:34:03] Enabling bundled linux tools. [00:34:03] Found bwa - /usr/local/bin/bwa [00:34:03] Found bcftools - /usr/local/bin/bcftools [00:34:03] Found samtools - /usr/local/bin/samtools [00:34:03] Found java - /usr/local/bin/java [00:34:03] Found snpEff - /usr/local/bin/snpEff [00:34:03] Found samclip - /usr/local/bin/samclip [00:34:03] Found seqtk - /usr/local/bin/seqtk [00:34:03] Found parallel - /usr/local/bin/parallel [00:34:03] Found freebayes - /usr/local/bin/freebayes [00:34:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:34:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:34:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:34:03] Found vcfuniq - /usr/local/bin/vcfuniq [00:34:03] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:34:03] Found gzip - /bin/gzip [00:34:03] Found vt - /usr/local/bin/vt [00:34:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:34:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:34:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:34:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:34:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:34:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:34:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:34:04] Please supply a reference FASTA/GBK/EMBL file with --reference
2[00:34:21] This is snippy 4.6.0
Show full stderr[00:34:21] This is snippy 4.6.0 [00:34:21] Written by Torsten Seemann [00:34:21] Obtained from https://github.com/tseemann/snippy [00:34:21] Detected operating system: linux [00:34:21] Enabling bundled linux tools. [00:34:21] Found bwa - /usr/local/bin/bwa [00:34:21] Found bcftools - /usr/local/bin/bcftools [00:34:21] Found samtools - /usr/local/bin/samtools [00:34:21] Found java - /usr/local/bin/java [00:34:21] Found snpEff - /usr/local/bin/snpEff [00:34:21] Found samclip - /usr/local/bin/samclip [00:34:21] Found seqtk - /usr/local/bin/seqtk [00:34:21] Found parallel - /usr/local/bin/parallel [00:34:21] Found freebayes - /usr/local/bin/freebayes [00:34:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:34:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:34:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:34:21] Found vcfuniq - /usr/local/bin/vcfuniq [00:34:21] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:34:21] Found gzip - /bin/gzip [00:34:21] Found vt - /usr/local/bin/vt [00:34:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:34:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:34:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:34:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:34:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:34:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:34:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:34:22] Please supply a reference FASTA/GBK/EMBL file with --reference
2[01:31:06] This is snippy 4.6.0
Show full stderr[01:31:06] This is snippy 4.6.0 [01:31:06] Written by Torsten Seemann [01:31:06] Obtained from https://github.com/tseemann/snippy [01:31:06] Detected operating system: linux [01:31:06] Enabling bundled linux tools. [01:31:06] Found bwa - /usr/local/bin/bwa [01:31:06] Found bcftools - /usr/local/bin/bcftools [01:31:06] Found samtools - /usr/local/bin/samtools [01:31:06] Found java - /usr/local/bin/java [01:31:06] Found snpEff - /usr/local/bin/snpEff [01:31:06] Found samclip - /usr/local/bin/samclip [01:31:06] Found seqtk - /usr/local/bin/seqtk [01:31:06] Found parallel - /usr/local/bin/parallel [01:31:06] Found freebayes - /usr/local/bin/freebayes [01:31:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:31:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:31:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:31:06] Found vcfuniq - /usr/local/bin/vcfuniq [01:31:06] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:31:06] Found gzip - /bin/gzip [01:31:06] Found vt - /usr/local/bin/vt [01:31:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:31:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:31:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:31:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:31:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:31:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:31:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:31:07] Please supply a reference FASTA/GBK/EMBL file with --reference
2[01:00:22] This is snippy 4.6.0
Show full stderr[01:00:22] This is snippy 4.6.0 [01:00:22] Written by Torsten Seemann [01:00:22] Obtained from https://github.com/tseemann/snippy [01:00:22] Detected operating system: linux [01:00:22] Enabling bundled linux tools. [01:00:22] Found bwa - /usr/local/bin/bwa [01:00:22] Found bcftools - /usr/local/bin/bcftools [01:00:22] Found samtools - /usr/local/bin/samtools [01:00:22] Found java - /usr/local/bin/java [01:00:22] Found snpEff - /usr/local/bin/snpEff [01:00:22] Found samclip - /usr/local/bin/samclip [01:00:22] Found seqtk - /usr/local/bin/seqtk [01:00:22] Found parallel - /usr/local/bin/parallel [01:00:22] Found freebayes - /usr/local/bin/freebayes [01:00:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:00:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:00:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:00:22] Found vcfuniq - /usr/local/bin/vcfuniq [01:00:22] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:00:22] Found gzip - /bin/gzip [01:00:22] Found vt - /usr/local/bin/vt [01:00:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:00:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:00:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:00:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:00:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:00:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:00:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:00:23] Please supply a reference FASTA/GBK/EMBL file with --reference
2[08:55:01] This is snippy 4.6.0
Show full stderr[08:55:01] This is snippy 4.6.0 [08:55:01] Written by Torsten Seemann [08:55:01] Obtained from https://github.com/tseemann/snippy [08:55:01] Detected operating system: linux [08:55:01] Enabling bundled linux tools. [08:55:01] Found bwa - /usr/local/bin/bwa [08:55:01] Found bcftools - /usr/local/bin/bcftools [08:55:01] Found samtools - /usr/local/bin/samtools [08:55:01] Found java - /usr/local/bin/java [08:55:01] Found snpEff - /usr/local/bin/snpEff [08:55:01] Found samclip - /usr/local/bin/samclip [08:55:01] Found seqtk - /usr/local/bin/seqtk [08:55:01] Found parallel - /usr/local/bin/parallel [08:55:01] Found freebayes - /usr/local/bin/freebayes [08:55:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:55:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:55:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:55:01] Found vcfuniq - /usr/local/bin/vcfuniq [08:55:01] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:55:01] Found gzip - /bin/gzip [08:55:01] Found vt - /usr/local/bin/vt [08:55:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:55:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:55:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:55:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:55:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:55:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:55:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:55:02] Using reference: /corral4/main/objects/7/5/0/dataset_750a1866-e250-4785-864e-3176f0899da8.dat [08:55:02] Treating reference as 'genbank' format. [08:55:02] Will use 1 CPU cores. [08:55:02] Using read file: /corral4/main/objects/0/4/9/dataset_0497b5ba-1d9b-4e33-8e5d-487ce10cf95c.dat [08:55:02] Creating folder: PAK_resistant_Strain_zip [08:55:02] Changing working directory: PAK_resistant_Strain_zip [08:55:02] Creating reference folder: reference [08:55:02] Extracting FASTA and GFF from reference. [08:55:05] Wrote 1 sequences to ref.fa [08:55:05] Wrote 5867 features to ref.gff [08:55:05] Creating reference/snpeff.config [08:55:05] Freebayes will process 1 chunks of 6502546 bp, 1 chunks at a time. [08:55:05] Using BAM RG (Read Group) ID: PAK_resistant_Strain_zip [08:55:05] Running: samtools faidx reference/ref.fa 2>> snps.log [08:55:05] Running: bwa index reference/ref.fa 2>> snps.log [08:55:10] Error running command, check PAK_resistant_Strain_zip/snps.log
2[08:56:01] This is snippy 4.6.0
Show full stderr[08:56:01] This is snippy 4.6.0 [08:56:01] Written by Torsten Seemann [08:56:01] Obtained from https://github.com/tseemann/snippy [08:56:01] Detected operating system: linux [08:56:01] Enabling bundled linux tools. [08:56:01] Found bwa - /usr/local/bin/bwa [08:56:01] Found bcftools - /usr/local/bin/bcftools [08:56:01] Found samtools - /usr/local/bin/samtools [08:56:01] Found java - /usr/local/bin/java [08:56:01] Found snpEff - /usr/local/bin/snpEff [08:56:01] Found samclip - /usr/local/bin/samclip [08:56:01] Found seqtk - /usr/local/bin/seqtk [08:56:01] Found parallel - /usr/local/bin/parallel [08:56:01] Found freebayes - /usr/local/bin/freebayes [08:56:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:56:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:56:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:56:01] Found vcfuniq - /usr/local/bin/vcfuniq [08:56:01] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:56:01] Found gzip - /bin/gzip [08:56:01] Found vt - /usr/local/bin/vt [08:56:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:56:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:56:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:56:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:56:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:56:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:56:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:56:01] Using reference: /corral4/main/objects/4/a/f/dataset_4af21818-52fd-41ed-b756-3780f3f34fd3.dat [08:56:01] Treating reference as 'genbank' format. [08:56:01] Will use 1 CPU cores. [08:56:01] Using read file: /corral4/main/objects/3/1/3/dataset_3133fc9f-f54e-447d-8f0e-2b980a1bc605.dat [08:56:01] Creating folder: PAK_resistant_Strain_zip [08:56:01] Changing working directory: PAK_resistant_Strain_zip [08:56:01] Creating reference folder: reference [08:56:01] Extracting FASTA and GFF from reference. [08:56:05] Wrote 1 sequences to ref.fa [08:56:05] Wrote 5867 features to ref.gff [08:56:05] Creating reference/snpeff.config [08:56:05] Freebayes will process 1 chunks of 6502546 bp, 1 chunks at a time. [08:56:05] Using BAM RG (Read Group) ID: PAK_resistant_Strain_zip [08:56:05] Running: samtools faidx reference/ref.fa 2>> snps.log [08:56:05] Running: bwa index reference/ref.fa 2>> snps.log [08:56:09] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [08:56:09] Running: ln -sf reference/ref.fa . 2>> snps.log [08:56:09] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [08:56:09] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [08:56:09] Running: snpEff build -c reference/snpeff.config -dataDir . -gff3 ref 2>> snps.log [08:56:15] Running: bwa mem -Y -M -R '@RG\tID:PAK_resistant_Strain_zip\tSM:PAK_resistant_Strain_zip' -t 1 reference/ref.fa /corral4/main/objects/3/1/3/dataset_3133fc9f-f54e-447d-8f0e-2b980a1bc605.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/073/013/73013944/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/073/013/73013944/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/073/013/73013944/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 1 sequences
2[08:58:26] This is snippy 4.6.0
Show full stderr[08:58:26] This is snippy 4.6.0 [08:58:26] Written by Torsten Seemann [08:58:26] Obtained from https://github.com/tseemann/snippy [08:58:26] Detected operating system: linux [08:58:26] Enabling bundled linux tools. [08:58:26] Found bwa - /usr/local/bin/bwa [08:58:26] Found bcftools - /usr/local/bin/bcftools [08:58:26] Found samtools - /usr/local/bin/samtools [08:58:26] Found java - /usr/local/bin/java [08:58:26] Found snpEff - /usr/local/bin/snpEff [08:58:26] Found samclip - /usr/local/bin/samclip [08:58:26] Found seqtk - /usr/local/bin/seqtk [08:58:26] Found parallel - /usr/local/bin/parallel [08:58:26] Found freebayes - /usr/local/bin/freebayes [08:58:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:58:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:58:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:58:26] Found vcfuniq - /usr/local/bin/vcfuniq [08:58:26] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:58:26] Found gzip - /bin/gzip [08:58:26] Found vt - /usr/local/bin/vt [08:58:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:58:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:58:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:58:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:58:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:58:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:58:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:58:27] Using reference: /corral4/main/objects/7/e/4/dataset_7e4b9f0c-299c-4b3c-a179-d1102993c678.dat [08:58:27] Treating reference as 'genbank' format. [08:58:27] Will use 1 CPU cores. [08:58:27] Using read file: /corral4/main/objects/1/8/8/dataset_18865a20-ae2d-4536-9508-ef198472e7e4.dat [08:58:27] Creating folder: PAK_resistant_Strain_zip [08:58:27] Changing working directory: PAK_resistant_Strain_zip [08:58:27] Creating reference folder: reference [08:58:27] Extracting FASTA and GFF from reference. [08:58:30] Wrote 1 sequences to ref.fa [08:58:30] Wrote 5867 features to ref.gff [08:58:30] Creating reference/snpeff.config [08:58:31] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time. [08:58:31] Using BAM RG (Read Group) ID: PAK_resistant_Strain_zip [08:58:31] Running: samtools faidx reference/ref.fa 2>> snps.log [08:58:31] Error running command, check PAK_resistant_Strain_zip/snps.log
2[21:22:23] This is snippy 4.6.0
Show full stderr[21:22:23] This is snippy 4.6.0 [21:22:23] Written by Torsten Seemann [21:22:23] Obtained from https://github.com/tseemann/snippy [21:22:23] Detected operating system: linux [21:22:23] Enabling bundled linux tools. [21:22:23] Found bwa - /usr/local/bin/bwa [21:22:23] Found bcftools - /usr/local/bin/bcftools [21:22:23] Found samtools - /usr/local/bin/samtools [21:22:23] Found java - /usr/local/bin/java [21:22:23] Found snpEff - /usr/local/bin/snpEff [21:22:23] Found samclip - /usr/local/bin/samclip [21:22:23] Found seqtk - /usr/local/bin/seqtk [21:22:23] Found parallel - /usr/local/bin/parallel [21:22:23] Found freebayes - /usr/local/bin/freebayes [21:22:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:22:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:22:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:22:23] Found vcfuniq - /usr/local/bin/vcfuniq [21:22:23] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:22:23] Found gzip - /bin/gzip [21:22:23] Found vt - /usr/local/bin/vt [21:22:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:22:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:22:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:22:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:22:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:22:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:22:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:22:25] Please supply a reference FASTA/GBK/EMBL file with --reference
2[21:22:16] This is snippy 4.6.0
Show full stderr[21:22:16] This is snippy 4.6.0 [21:22:16] Written by Torsten Seemann [21:22:16] Obtained from https://github.com/tseemann/snippy [21:22:16] Detected operating system: linux [21:22:16] Enabling bundled linux tools. [21:22:16] Found bwa - /usr/local/bin/bwa [21:22:16] Found bcftools - /usr/local/bin/bcftools [21:22:16] Found samtools - /usr/local/bin/samtools [21:22:16] Found java - /usr/local/bin/java [21:22:16] Found snpEff - /usr/local/bin/snpEff [21:22:16] Found samclip - /usr/local/bin/samclip [21:22:16] Found seqtk - /usr/local/bin/seqtk [21:22:16] Found parallel - /usr/local/bin/parallel [21:22:16] Found freebayes - /usr/local/bin/freebayes [21:22:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:22:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:22:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:22:16] Found vcfuniq - /usr/local/bin/vcfuniq [21:22:16] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:22:16] Found gzip - /bin/gzip [21:22:16] Found vt - /usr/local/bin/vt [21:22:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:22:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:22:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:22:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:22:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:22:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:22:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:22:17] Please supply a reference FASTA/GBK/EMBL file with --reference
2[21:27:46] This is snippy 4.6.0
Show full stderr[21:27:46] This is snippy 4.6.0 [21:27:46] Written by Torsten Seemann [21:27:46] Obtained from https://github.com/tseemann/snippy [21:27:46] Detected operating system: linux [21:27:46] Enabling bundled linux tools. [21:27:46] Found bwa - /usr/local/bin/bwa [21:27:46] Found bcftools - /usr/local/bin/bcftools [21:27:46] Found samtools - /usr/local/bin/samtools [21:27:46] Found java - /usr/local/bin/java [21:27:46] Found snpEff - /usr/local/bin/snpEff [21:27:46] Found samclip - /usr/local/bin/samclip [21:27:46] Found seqtk - /usr/local/bin/seqtk [21:27:46] Found parallel - /usr/local/bin/parallel [21:27:46] Found freebayes - /usr/local/bin/freebayes [21:27:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:27:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:27:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:27:46] Found vcfuniq - /usr/local/bin/vcfuniq [21:27:46] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:27:46] Found gzip - /bin/gzip [21:27:46] Found vt - /usr/local/bin/vt [21:27:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:27:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:27:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:27:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:27:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:27:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:27:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:27:47] Please supply a reference FASTA/GBK/EMBL file with --reference
2[05:57:18] This is snippy 4.6.0
Show full stderr[05:57:18] This is snippy 4.6.0 [05:57:18] Written by Torsten Seemann [05:57:18] Obtained from https://github.com/tseemann/snippy [05:57:18] Detected operating system: linux [05:57:18] Enabling bundled linux tools. [05:57:18] Found bwa - /usr/local/bin/bwa [05:57:18] Found bcftools - /usr/local/bin/bcftools [05:57:18] Found samtools - /usr/local/bin/samtools [05:57:18] Found java - /usr/local/bin/java [05:57:18] Found snpEff - /usr/local/bin/snpEff [05:57:18] Found samclip - /usr/local/bin/samclip [05:57:18] Found seqtk - /usr/local/bin/seqtk [05:57:18] Found parallel - /usr/local/bin/parallel [05:57:18] Found freebayes - /usr/local/bin/freebayes [05:57:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:57:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:57:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:57:18] Found vcfuniq - /usr/local/bin/vcfuniq [05:57:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:57:18] Found gzip - /bin/gzip [05:57:18] Found vt - /usr/local/bin/vt [05:57:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:57:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:57:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:57:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:57:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:57:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:57:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:57:20] Please supply a reference FASTA/GBK/EMBL file with --reference
2[05:57:17] This is snippy 4.6.0
Show full stderr[05:57:17] This is snippy 4.6.0 [05:57:17] Written by Torsten Seemann [05:57:17] Obtained from https://github.com/tseemann/snippy [05:57:17] Detected operating system: linux [05:57:17] Enabling bundled linux tools. [05:57:17] Found bwa - /usr/local/bin/bwa [05:57:17] Found bcftools - /usr/local/bin/bcftools [05:57:17] Found samtools - /usr/local/bin/samtools [05:57:17] Found java - /usr/local/bin/java [05:57:17] Found snpEff - /usr/local/bin/snpEff [05:57:17] Found samclip - /usr/local/bin/samclip [05:57:17] Found seqtk - /usr/local/bin/seqtk [05:57:17] Found parallel - /usr/local/bin/parallel [05:57:17] Found freebayes - /usr/local/bin/freebayes [05:57:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:57:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:57:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:57:17] Found vcfuniq - /usr/local/bin/vcfuniq [05:57:17] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:57:17] Found gzip - /bin/gzip [05:57:17] Found vt - /usr/local/bin/vt [05:57:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:57:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:57:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:57:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:57:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:57:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:57:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:57:18] Please supply a reference FASTA/GBK/EMBL file with --reference
1[21:24:12] This is snippy 4.6.0
Show full stderr[21:24:12] This is snippy 4.6.0 [21:24:12] Written by Torsten Seemann [21:24:12] Obtained from https://github.com/tseemann/snippy [21:24:12] Detected operating system: linux [21:24:12] Enabling bundled linux tools. [21:24:12] Found bwa - /usr/local/bin/bwa [21:24:12] Found bcftools - /usr/local/bin/bcftools [21:24:12] Found samtools - /usr/local/bin/samtools [21:24:12] Found java - /usr/local/bin/java [21:24:12] Found snpEff - /usr/local/bin/snpEff [21:24:12] Found samclip - /usr/local/bin/samclip [21:24:12] Found seqtk - /usr/local/bin/seqtk [21:24:12] Found parallel - /usr/local/bin/parallel [21:24:12] Found freebayes - /usr/local/bin/freebayes [21:24:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:24:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:24:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:24:12] Found vcfuniq - /usr/local/bin/vcfuniq [21:24:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:24:12] Found gzip - /bin/gzip [21:24:12] Found vt - /usr/local/bin/vt [21:24:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:24:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:24:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:24:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:24:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:24:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:24:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:24:13] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat [21:24:13] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat'
1[21:24:15] This is snippy 4.6.0
Show full stderr[21:24:15] This is snippy 4.6.0 [21:24:15] Written by Torsten Seemann [21:24:15] Obtained from https://github.com/tseemann/snippy [21:24:15] Detected operating system: linux [21:24:15] Enabling bundled linux tools. [21:24:15] Found bwa - /usr/local/bin/bwa [21:24:15] Found bcftools - /usr/local/bin/bcftools [21:24:15] Found samtools - /usr/local/bin/samtools [21:24:15] Found java - /usr/local/bin/java [21:24:15] Found snpEff - /usr/local/bin/snpEff [21:24:15] Found samclip - /usr/local/bin/samclip [21:24:15] Found seqtk - /usr/local/bin/seqtk [21:24:15] Found parallel - /usr/local/bin/parallel [21:24:15] Found freebayes - /usr/local/bin/freebayes [21:24:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:24:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:24:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:24:15] Found vcfuniq - /usr/local/bin/vcfuniq [21:24:15] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:24:15] Found gzip - /bin/gzip [21:24:15] Found vt - /usr/local/bin/vt [21:24:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:24:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:24:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:24:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:24:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:24:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:24:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:24:17] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat [21:24:17] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat'
1[21:24:19] This is snippy 4.6.0
Show full stderr[21:24:19] This is snippy 4.6.0 [21:24:19] Written by Torsten Seemann [21:24:19] Obtained from https://github.com/tseemann/snippy [21:24:19] Detected operating system: linux [21:24:19] Enabling bundled linux tools. [21:24:19] Found bwa - /usr/local/bin/bwa [21:24:19] Found bcftools - /usr/local/bin/bcftools [21:24:19] Found samtools - /usr/local/bin/samtools [21:24:19] Found java - /usr/local/bin/java [21:24:19] Found snpEff - /usr/local/bin/snpEff [21:24:19] Found samclip - /usr/local/bin/samclip [21:24:19] Found seqtk - /usr/local/bin/seqtk [21:24:19] Found parallel - /usr/local/bin/parallel [21:24:19] Found freebayes - /usr/local/bin/freebayes [21:24:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:24:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:24:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:24:19] Found vcfuniq - /usr/local/bin/vcfuniq [21:24:19] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:24:19] Found gzip - /bin/gzip [21:24:19] Found vt - /usr/local/bin/vt [21:24:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:24:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:24:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:24:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:24:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:24:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:24:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:24:20] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat [21:24:20] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat'
1[21:24:17] This is snippy 4.6.0
Show full stderr[21:24:17] This is snippy 4.6.0 [21:24:17] Written by Torsten Seemann [21:24:17] Obtained from https://github.com/tseemann/snippy [21:24:17] Detected operating system: linux [21:24:17] Enabling bundled linux tools. [21:24:17] Found bwa - /usr/local/bin/bwa [21:24:17] Found bcftools - /usr/local/bin/bcftools [21:24:17] Found samtools - /usr/local/bin/samtools [21:24:17] Found java - /usr/local/bin/java [21:24:17] Found snpEff - /usr/local/bin/snpEff [21:24:17] Found samclip - /usr/local/bin/samclip [21:24:17] Found seqtk - /usr/local/bin/seqtk [21:24:17] Found parallel - /usr/local/bin/parallel [21:24:17] Found freebayes - /usr/local/bin/freebayes [21:24:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:24:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:24:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:24:17] Found vcfuniq - /usr/local/bin/vcfuniq [21:24:17] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:24:17] Found gzip - /bin/gzip [21:24:17] Found vt - /usr/local/bin/vt [21:24:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:24:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:24:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:24:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:24:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:24:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:24:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:24:18] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat [21:24:18] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat'
1[21:24:30] This is snippy 4.6.0
Show full stderr[21:24:30] This is snippy 4.6.0 [21:24:30] Written by Torsten Seemann [21:24:30] Obtained from https://github.com/tseemann/snippy [21:24:30] Detected operating system: linux [21:24:30] Enabling bundled linux tools. [21:24:30] Found bwa - /usr/local/bin/bwa [21:24:30] Found bcftools - /usr/local/bin/bcftools [21:24:30] Found samtools - /usr/local/bin/samtools [21:24:30] Found java - /usr/local/bin/java [21:24:30] Found snpEff - /usr/local/bin/snpEff [21:24:30] Found samclip - /usr/local/bin/samclip [21:24:30] Found seqtk - /usr/local/bin/seqtk [21:24:30] Found parallel - /usr/local/bin/parallel [21:24:30] Found freebayes - /usr/local/bin/freebayes [21:24:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:24:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:24:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:24:30] Found vcfuniq - /usr/local/bin/vcfuniq [21:24:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:24:30] Found gzip - /bin/gzip [21:24:30] Found vt - /usr/local/bin/vt [21:24:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:24:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:24:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:24:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:24:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:24:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:24:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:24:31] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat [21:24:31] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat'
1[21:24:32] This is snippy 4.6.0
Show full stderr[21:24:32] This is snippy 4.6.0 [21:24:32] Written by Torsten Seemann [21:24:32] Obtained from https://github.com/tseemann/snippy [21:24:32] Detected operating system: linux [21:24:32] Enabling bundled linux tools. [21:24:32] Found bwa - /usr/local/bin/bwa [21:24:32] Found bcftools - /usr/local/bin/bcftools [21:24:32] Found samtools - /usr/local/bin/samtools [21:24:32] Found java - /usr/local/bin/java [21:24:32] Found snpEff - /usr/local/bin/snpEff [21:24:32] Found samclip - /usr/local/bin/samclip [21:24:32] Found seqtk - /usr/local/bin/seqtk [21:24:32] Found parallel - /usr/local/bin/parallel [21:24:32] Found freebayes - /usr/local/bin/freebayes [21:24:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:24:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:24:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:24:32] Found vcfuniq - /usr/local/bin/vcfuniq [21:24:32] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:24:32] Found gzip - /bin/gzip [21:24:32] Found vt - /usr/local/bin/vt [21:24:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:24:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:24:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:24:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:24:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:24:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:24:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:24:33] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat [21:24:33] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat'
1[21:25:05] This is snippy 4.6.0
Show full stderr[21:25:05] This is snippy 4.6.0 [21:25:05] Written by Torsten Seemann [21:25:05] Obtained from https://github.com/tseemann/snippy [21:25:05] Detected operating system: linux [21:25:05] Enabling bundled linux tools. [21:25:05] Found bwa - /usr/local/bin/bwa [21:25:05] Found bcftools - /usr/local/bin/bcftools [21:25:05] Found samtools - /usr/local/bin/samtools [21:25:05] Found java - /usr/local/bin/java [21:25:05] Found snpEff - /usr/local/bin/snpEff [21:25:05] Found samclip - /usr/local/bin/samclip [21:25:05] Found seqtk - /usr/local/bin/seqtk [21:25:05] Found parallel - /usr/local/bin/parallel [21:25:05] Found freebayes - /usr/local/bin/freebayes [21:25:05] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:25:05] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:25:05] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:25:05] Found vcfuniq - /usr/local/bin/vcfuniq [21:25:05] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:25:05] Found gzip - /bin/gzip [21:25:05] Found vt - /usr/local/bin/vt [21:25:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:25:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:25:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:25:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:25:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:25:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:25:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:25:06] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat [21:25:07] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat'
1[21:25:08] This is snippy 4.6.0
Show full stderr[21:25:08] This is snippy 4.6.0 [21:25:08] Written by Torsten Seemann [21:25:08] Obtained from https://github.com/tseemann/snippy [21:25:08] Detected operating system: linux [21:25:08] Enabling bundled linux tools. [21:25:08] Found bwa - /usr/local/bin/bwa [21:25:08] Found bcftools - /usr/local/bin/bcftools [21:25:08] Found samtools - /usr/local/bin/samtools [21:25:08] Found java - /usr/local/bin/java [21:25:08] Found snpEff - /usr/local/bin/snpEff [21:25:08] Found samclip - /usr/local/bin/samclip [21:25:08] Found seqtk - /usr/local/bin/seqtk [21:25:08] Found parallel - /usr/local/bin/parallel [21:25:08] Found freebayes - /usr/local/bin/freebayes [21:25:08] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:25:08] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:25:08] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:25:08] Found vcfuniq - /usr/local/bin/vcfuniq [21:25:08] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:25:08] Found gzip - /bin/gzip [21:25:08] Found vt - /usr/local/bin/vt [21:25:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:25:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:25:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:25:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:25:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:25:09] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:25:09] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:25:09] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat [21:25:09] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat'
1[21:34:14] This is snippy 4.6.0
Show full stderr[21:34:14] This is snippy 4.6.0 [21:34:14] Written by Torsten Seemann [21:34:14] Obtained from https://github.com/tseemann/snippy [21:34:14] Detected operating system: linux [21:34:14] Enabling bundled linux tools. [21:34:14] Found bwa - /usr/local/bin/bwa [21:34:14] Found bcftools - /usr/local/bin/bcftools [21:34:14] Found samtools - /usr/local/bin/samtools [21:34:14] Found java - /usr/local/bin/java [21:34:14] Found snpEff - /usr/local/bin/snpEff [21:34:14] Found samclip - /usr/local/bin/samclip [21:34:14] Found seqtk - /usr/local/bin/seqtk [21:34:14] Found parallel - /usr/local/bin/parallel [21:34:14] Found freebayes - /usr/local/bin/freebayes [21:34:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:34:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:34:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:34:14] Found vcfuniq - /usr/local/bin/vcfuniq [21:34:14] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:34:14] Found gzip - /bin/gzip [21:34:14] Found vt - /usr/local/bin/vt [21:34:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:34:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:34:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:34:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:34:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:34:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:34:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:34:15] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat [21:34:15] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat'
1[21:34:34] This is snippy 4.6.0
Show full stderr[21:34:34] This is snippy 4.6.0 [21:34:34] Written by Torsten Seemann [21:34:34] Obtained from https://github.com/tseemann/snippy [21:34:34] Detected operating system: linux [21:34:34] Enabling bundled linux tools. [21:34:34] Found bwa - /usr/local/bin/bwa [21:34:34] Found bcftools - /usr/local/bin/bcftools [21:34:34] Found samtools - /usr/local/bin/samtools [21:34:34] Found java - /usr/local/bin/java [21:34:34] Found snpEff - /usr/local/bin/snpEff [21:34:34] Found samclip - /usr/local/bin/samclip [21:34:34] Found seqtk - /usr/local/bin/seqtk [21:34:34] Found parallel - /usr/local/bin/parallel [21:34:34] Found freebayes - /usr/local/bin/freebayes [21:34:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:34:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:34:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:34:34] Found vcfuniq - /usr/local/bin/vcfuniq [21:34:34] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:34:34] Found gzip - /bin/gzip [21:34:34] Found vt - /usr/local/bin/vt [21:34:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:34:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:34:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:34:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:34:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:34:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:34:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:34:35] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat [21:34:35] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat'
1[21:34:59] This is snippy 4.6.0
Show full stderr[21:34:59] This is snippy 4.6.0 [21:34:59] Written by Torsten Seemann [21:34:59] Obtained from https://github.com/tseemann/snippy [21:34:59] Detected operating system: linux [21:34:59] Enabling bundled linux tools. [21:34:59] Found bwa - /usr/local/bin/bwa [21:34:59] Found bcftools - /usr/local/bin/bcftools [21:34:59] Found samtools - /usr/local/bin/samtools [21:34:59] Found java - /usr/local/bin/java [21:34:59] Found snpEff - /usr/local/bin/snpEff [21:34:59] Found samclip - /usr/local/bin/samclip [21:34:59] Found seqtk - /usr/local/bin/seqtk [21:34:59] Found parallel - /usr/local/bin/parallel [21:34:59] Found freebayes - /usr/local/bin/freebayes [21:34:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:34:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:34:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:34:59] Found vcfuniq - /usr/local/bin/vcfuniq [21:34:59] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:34:59] Found gzip - /bin/gzip [21:34:59] Found vt - /usr/local/bin/vt [21:34:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:34:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:34:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:34:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:34:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:35:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:35:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:35:00] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat [21:35:00] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat'
1[21:35:00] This is snippy 4.6.0
Show full stderr[21:35:00] This is snippy 4.6.0 [21:35:00] Written by Torsten Seemann [21:35:00] Obtained from https://github.com/tseemann/snippy [21:35:00] Detected operating system: linux [21:35:00] Enabling bundled linux tools. [21:35:00] Found bwa - /usr/local/bin/bwa [21:35:00] Found bcftools - /usr/local/bin/bcftools [21:35:00] Found samtools - /usr/local/bin/samtools [21:35:00] Found java - /usr/local/bin/java [21:35:00] Found snpEff - /usr/local/bin/snpEff [21:35:00] Found samclip - /usr/local/bin/samclip [21:35:00] Found seqtk - /usr/local/bin/seqtk [21:35:00] Found parallel - /usr/local/bin/parallel [21:35:00] Found freebayes - /usr/local/bin/freebayes [21:35:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:35:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:35:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:35:00] Found vcfuniq - /usr/local/bin/vcfuniq [21:35:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:35:00] Found gzip - /bin/gzip [21:35:00] Found vt - /usr/local/bin/vt [21:35:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:35:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:35:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:35:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:35:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:35:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:35:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:35:01] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat [21:35:01] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat'
1[21:35:14] This is snippy 4.6.0
Show full stderr[21:35:14] This is snippy 4.6.0 [21:35:14] Written by Torsten Seemann [21:35:14] Obtained from https://github.com/tseemann/snippy [21:35:14] Detected operating system: linux [21:35:14] Enabling bundled linux tools. [21:35:14] Found bwa - /usr/local/bin/bwa [21:35:14] Found bcftools - /usr/local/bin/bcftools [21:35:14] Found samtools - /usr/local/bin/samtools [21:35:14] Found java - /usr/local/bin/java [21:35:14] Found snpEff - /usr/local/bin/snpEff [21:35:14] Found samclip - /usr/local/bin/samclip [21:35:14] Found seqtk - /usr/local/bin/seqtk [21:35:14] Found parallel - /usr/local/bin/parallel [21:35:14] Found freebayes - /usr/local/bin/freebayes [21:35:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:35:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:35:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:35:14] Found vcfuniq - /usr/local/bin/vcfuniq [21:35:14] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:35:14] Found gzip - /bin/gzip [21:35:14] Found vt - /usr/local/bin/vt [21:35:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:35:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:35:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:35:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:35:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:35:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:35:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:35:15] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat [21:35:15] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat'
1[21:35:17] This is snippy 4.6.0
Show full stderr[21:35:17] This is snippy 4.6.0 [21:35:17] Written by Torsten Seemann [21:35:17] Obtained from https://github.com/tseemann/snippy [21:35:17] Detected operating system: linux [21:35:17] Enabling bundled linux tools. [21:35:17] Found bwa - /usr/local/bin/bwa [21:35:17] Found bcftools - /usr/local/bin/bcftools [21:35:17] Found samtools - /usr/local/bin/samtools [21:35:17] Found java - /usr/local/bin/java [21:35:17] Found snpEff - /usr/local/bin/snpEff [21:35:17] Found samclip - /usr/local/bin/samclip [21:35:17] Found seqtk - /usr/local/bin/seqtk [21:35:17] Found parallel - /usr/local/bin/parallel [21:35:17] Found freebayes - /usr/local/bin/freebayes [21:35:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:35:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:35:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:35:17] Found vcfuniq - /usr/local/bin/vcfuniq [21:35:17] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:35:17] Found gzip - /bin/gzip [21:35:17] Found vt - /usr/local/bin/vt [21:35:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:35:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:35:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:35:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:35:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:35:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:35:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:35:18] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat [21:35:18] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat'
1[21:35:20] This is snippy 4.6.0
Show full stderr[21:35:20] This is snippy 4.6.0 [21:35:20] Written by Torsten Seemann [21:35:20] Obtained from https://github.com/tseemann/snippy [21:35:20] Detected operating system: linux [21:35:20] Enabling bundled linux tools. [21:35:20] Found bwa - /usr/local/bin/bwa [21:35:20] Found bcftools - /usr/local/bin/bcftools [21:35:20] Found samtools - /usr/local/bin/samtools [21:35:20] Found java - /usr/local/bin/java [21:35:20] Found snpEff - /usr/local/bin/snpEff [21:35:20] Found samclip - /usr/local/bin/samclip [21:35:20] Found seqtk - /usr/local/bin/seqtk [21:35:20] Found parallel - /usr/local/bin/parallel [21:35:20] Found freebayes - /usr/local/bin/freebayes [21:35:20] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:35:20] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:35:20] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:35:20] Found vcfuniq - /usr/local/bin/vcfuniq [21:35:20] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:35:20] Found gzip - /bin/gzip [21:35:20] Found vt - /usr/local/bin/vt [21:35:20] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:35:20] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:35:20] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:35:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:35:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:35:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:35:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:35:21] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat [21:35:21] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat'
1[21:34:46] This is snippy 4.6.0
Show full stderr[21:34:46] This is snippy 4.6.0 [21:34:46] Written by Torsten Seemann [21:34:46] Obtained from https://github.com/tseemann/snippy [21:34:46] Detected operating system: linux [21:34:46] Enabling bundled linux tools. [21:34:46] Found bwa - /usr/local/bin/bwa [21:34:46] Found bcftools - /usr/local/bin/bcftools [21:34:46] Found samtools - /usr/local/bin/samtools [21:34:46] Found java - /usr/local/bin/java [21:34:46] Found snpEff - /usr/local/bin/snpEff [21:34:46] Found samclip - /usr/local/bin/samclip [21:34:46] Found seqtk - /usr/local/bin/seqtk [21:34:46] Found parallel - /usr/local/bin/parallel [21:34:46] Found freebayes - /usr/local/bin/freebayes [21:34:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:34:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:34:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:34:46] Found vcfuniq - /usr/local/bin/vcfuniq [21:34:46] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:34:46] Found gzip - /bin/gzip [21:34:46] Found vt - /usr/local/bin/vt [21:34:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:34:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:34:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:34:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:34:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:34:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:34:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:34:47] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat [21:34:47] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat'
1[21:34:56] This is snippy 4.6.0
Show full stderr[21:34:56] This is snippy 4.6.0 [21:34:56] Written by Torsten Seemann [21:34:56] Obtained from https://github.com/tseemann/snippy [21:34:56] Detected operating system: linux [21:34:56] Enabling bundled linux tools. [21:34:56] Found bwa - /usr/local/bin/bwa [21:34:56] Found bcftools - /usr/local/bin/bcftools [21:34:56] Found samtools - /usr/local/bin/samtools [21:34:57] Found java - /usr/local/bin/java [21:34:57] Found snpEff - /usr/local/bin/snpEff [21:34:57] Found samclip - /usr/local/bin/samclip [21:34:57] Found seqtk - /usr/local/bin/seqtk [21:34:57] Found parallel - /usr/local/bin/parallel [21:34:57] Found freebayes - /usr/local/bin/freebayes [21:34:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:34:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:34:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:34:57] Found vcfuniq - /usr/local/bin/vcfuniq [21:34:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:34:57] Found gzip - /bin/gzip [21:34:57] Found vt - /usr/local/bin/vt [21:34:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:34:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:34:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:34:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:34:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:34:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:34:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:34:58] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat [21:34:58] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat'
1[21:35:02] This is snippy 4.6.0
Show full stderr[21:35:02] This is snippy 4.6.0 [21:35:02] Written by Torsten Seemann [21:35:02] Obtained from https://github.com/tseemann/snippy [21:35:02] Detected operating system: linux [21:35:02] Enabling bundled linux tools. [21:35:02] Found bwa - /usr/local/bin/bwa [21:35:02] Found bcftools - /usr/local/bin/bcftools [21:35:02] Found samtools - /usr/local/bin/samtools [21:35:02] Found java - /usr/local/bin/java [21:35:02] Found snpEff - /usr/local/bin/snpEff [21:35:02] Found samclip - /usr/local/bin/samclip [21:35:02] Found seqtk - /usr/local/bin/seqtk [21:35:02] Found parallel - /usr/local/bin/parallel [21:35:02] Found freebayes - /usr/local/bin/freebayes [21:35:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:35:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:35:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:35:02] Found vcfuniq - /usr/local/bin/vcfuniq [21:35:02] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:35:02] Found gzip - /bin/gzip [21:35:02] Found vt - /usr/local/bin/vt [21:35:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:35:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:35:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:35:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:35:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:35:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:35:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:35:03] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat [21:35:03] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat'
1[21:35:23] This is snippy 4.6.0
Show full stderr[21:35:23] This is snippy 4.6.0 [21:35:23] Written by Torsten Seemann [21:35:23] Obtained from https://github.com/tseemann/snippy [21:35:23] Detected operating system: linux [21:35:23] Enabling bundled linux tools. [21:35:23] Found bwa - /usr/local/bin/bwa [21:35:23] Found bcftools - /usr/local/bin/bcftools [21:35:23] Found samtools - /usr/local/bin/samtools [21:35:23] Found java - /usr/local/bin/java [21:35:23] Found snpEff - /usr/local/bin/snpEff [21:35:23] Found samclip - /usr/local/bin/samclip [21:35:23] Found seqtk - /usr/local/bin/seqtk [21:35:23] Found parallel - /usr/local/bin/parallel [21:35:23] Found freebayes - /usr/local/bin/freebayes [21:35:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:35:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:35:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:35:23] Found vcfuniq - /usr/local/bin/vcfuniq [21:35:23] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:35:24] Found gzip - /bin/gzip [21:35:24] Found vt - /usr/local/bin/vt [21:35:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:35:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:35:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:35:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:35:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:35:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:35:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:35:25] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat [21:35:25] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat'
1[21:35:32] This is snippy 4.6.0
Show full stderr[21:35:32] This is snippy 4.6.0 [21:35:32] Written by Torsten Seemann [21:35:32] Obtained from https://github.com/tseemann/snippy [21:35:32] Detected operating system: linux [21:35:32] Enabling bundled linux tools. [21:35:32] Found bwa - /usr/local/bin/bwa [21:35:32] Found bcftools - /usr/local/bin/bcftools [21:35:32] Found samtools - /usr/local/bin/samtools [21:35:32] Found java - /usr/local/bin/java [21:35:32] Found snpEff - /usr/local/bin/snpEff [21:35:32] Found samclip - /usr/local/bin/samclip [21:35:32] Found seqtk - /usr/local/bin/seqtk [21:35:32] Found parallel - /usr/local/bin/parallel [21:35:32] Found freebayes - /usr/local/bin/freebayes [21:35:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:35:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:35:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:35:32] Found vcfuniq - /usr/local/bin/vcfuniq [21:35:32] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:35:32] Found gzip - /bin/gzip [21:35:32] Found vt - /usr/local/bin/vt [21:35:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:35:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:35:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:35:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:35:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:35:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:35:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:35:33] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat [21:35:33] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat'
1[21:35:33] This is snippy 4.6.0
Show full stderr[21:35:33] This is snippy 4.6.0 [21:35:33] Written by Torsten Seemann [21:35:33] Obtained from https://github.com/tseemann/snippy [21:35:33] Detected operating system: linux [21:35:33] Enabling bundled linux tools. [21:35:33] Found bwa - /usr/local/bin/bwa [21:35:33] Found bcftools - /usr/local/bin/bcftools [21:35:33] Found samtools - /usr/local/bin/samtools [21:35:33] Found java - /usr/local/bin/java [21:35:33] Found snpEff - /usr/local/bin/snpEff [21:35:33] Found samclip - /usr/local/bin/samclip [21:35:33] Found seqtk - /usr/local/bin/seqtk [21:35:33] Found parallel - /usr/local/bin/parallel [21:35:33] Found freebayes - /usr/local/bin/freebayes [21:35:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:35:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:35:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:35:33] Found vcfuniq - /usr/local/bin/vcfuniq [21:35:33] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:35:33] Found gzip - /bin/gzip [21:35:33] Found vt - /usr/local/bin/vt [21:35:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:35:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:35:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:35:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:35:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:35:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:35:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:35:34] Using reference: /corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat [21:35:34] Could not guess format '/corral4/main/objects/4/e/f/dataset_4efbc29c-8e5a-4db6-bc4b-012fcbd0b61d.dat'
1[22:05:20] This is snippy 4.6.0
Show full stderr[22:05:20] This is snippy 4.6.0 [22:05:20] Written by Torsten Seemann [22:05:20] Obtained from https://github.com/tseemann/snippy [22:05:20] Detected operating system: linux [22:05:20] Enabling bundled linux tools. [22:05:20] Found bwa - /usr/local/bin/bwa [22:05:20] Found bcftools - /usr/local/bin/bcftools [22:05:20] Found samtools - /usr/local/bin/samtools [22:05:20] Found java - /usr/local/bin/java [22:05:20] Found snpEff - /usr/local/bin/snpEff [22:05:20] Found samclip - /usr/local/bin/samclip [22:05:20] Found seqtk - /usr/local/bin/seqtk [22:05:20] Found parallel - /usr/local/bin/parallel [22:05:20] Found freebayes - /usr/local/bin/freebayes [22:05:20] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [22:05:20] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [22:05:20] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [22:05:20] Found vcfuniq - /usr/local/bin/vcfuniq [22:05:20] Found vcffirstheader - /usr/local/bin/vcffirstheader [22:05:20] Found gzip - /bin/gzip [22:05:20] Found vt - /usr/local/bin/vt [22:05:20] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [22:05:20] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [22:05:20] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [22:05:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [22:05:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [22:05:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [22:05:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [22:05:21] Using reference: /jetstream2/scratch/main/jobs/72172731/inputs/dataset_c3278295-0534-4341-a983-519e27d93d98.dat [22:05:21] Treating reference as 'fasta' format. [22:05:21] Will use 1 CPU cores. [22:05:21] Using read file: /jetstream2/scratch/main/jobs/72172731/inputs/dataset_eaf88053-c6c7-4573-935e-0a20a2a2f029.dat [22:05:21] Creating folder: Select_on_dataset_11 [22:05:21] Changing working directory: Select_on_dataset_11 [22:05:21] Creating reference folder: reference [22:05:21] Extracting FASTA and GFF from reference. [22:05:21] Wrote 1 sequences to ref.fa [22:05:21] Wrote 0 features to ref.gff [22:05:21] Freebayes will process 1 chunks of 12416664 bp, 1 chunks at a time. [22:05:21] Using BAM RG (Read Group) ID: Select_on_dataset_11 [22:05:21] Running: samtools faidx reference/ref.fa 2>> snps.log [22:05:21] Running: bwa index reference/ref.fa 2>> snps.log [22:05:25] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [22:05:25] Running: ln -sf reference/ref.fa . 2>> snps.log [22:05:25] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [22:05:25] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [22:05:25] Running: bwa mem -Y -M -R '@RG\tID:Select_on_dataset_11\tSM:Select_on_dataset_11' -t 1 reference/ref.fa /jetstream2/scratch/main/jobs/72172731/inputs/dataset_eaf88053-c6c7-4573-935e-0a20a2a2f029.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/72172731/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/72172731/tmp --threads 0 -m 12000M | samtools markdup -T /jetstream2/scratch/main/jobs/72172731/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] Found 1 sequences in reference/ref.fa.fai [M::process] read 1 sequences (11639536 bp)... [samclip] Total SAM records 0
1[23:56:35] This is snippy 4.6.0
Show full stderr[23:56:35] This is snippy 4.6.0 [23:56:35] Written by Torsten Seemann [23:56:35] Obtained from https://github.com/tseemann/snippy [23:56:35] Detected operating system: linux [23:56:35] Enabling bundled linux tools. [23:56:35] Found bwa - /usr/local/bin/bwa [23:56:35] Found bcftools - /usr/local/bin/bcftools [23:56:35] Found samtools - /usr/local/bin/samtools [23:56:35] Found java - /usr/local/bin/java [23:56:35] Found snpEff - /usr/local/bin/snpEff [23:56:35] Found samclip - /usr/local/bin/samclip [23:56:35] Found seqtk - /usr/local/bin/seqtk [23:56:35] Found parallel - /usr/local/bin/parallel [23:56:35] Found freebayes - /usr/local/bin/freebayes [23:56:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [23:56:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [23:56:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [23:56:35] Found vcfuniq - /usr/local/bin/vcfuniq [23:56:35] Found vcffirstheader - /usr/local/bin/vcffirstheader [23:56:35] Found gzip - /bin/gzip [23:56:35] Found vt - /usr/local/bin/vt [23:56:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [23:56:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [23:56:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [23:56:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [23:56:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [23:56:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [23:56:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [23:56:36] Using reference: /jetstream2/scratch/main/jobs/72174392/inputs/dataset_c3278295-0534-4341-a983-519e27d93d98.dat [23:56:36] Treating reference as 'fasta' format. [23:56:36] Will use 1 CPU cores. [23:56:36] Using read file: /jetstream2/scratch/main/jobs/72174392/inputs/dataset_eaf88053-c6c7-4573-935e-0a20a2a2f029.dat [23:56:36] Creating folder: Select_on_dataset_11 [23:56:36] Changing working directory: Select_on_dataset_11 [23:56:36] Creating reference folder: reference [23:56:36] Extracting FASTA and GFF from reference. [23:56:37] Wrote 1 sequences to ref.fa [23:56:37] Wrote 0 features to ref.gff [23:56:37] Freebayes will process 1 chunks of 12416664 bp, 1 chunks at a time. [23:56:37] Using BAM RG (Read Group) ID: Select_on_dataset_11 [23:56:37] Running: samtools faidx reference/ref.fa 2>> snps.log [23:56:37] Running: bwa index reference/ref.fa 2>> snps.log [23:56:43] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [23:56:43] Running: ln -sf reference/ref.fa . 2>> snps.log [23:56:43] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [23:56:43] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [23:56:43] Running: bwa mem -Y -M -R '@RG\tID:Select_on_dataset_11\tSM:Select_on_dataset_11' -t 1 reference/ref.fa /jetstream2/scratch/main/jobs/72174392/inputs/dataset_eaf88053-c6c7-4573-935e-0a20a2a2f029.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/72174392/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/72174392/tmp --threads 0 -m 12000M | samtools markdup -T /jetstream2/scratch/main/jobs/72174392/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 1 sequences in reference/ref.fa.fai [M::process] read 1 sequences (11639536 bp)... [samclip] Total SAM records 0
1[04:37:18] This is snippy 4.6.0
Show full stderr[04:37:18] This is snippy 4.6.0 [04:37:18] Written by Torsten Seemann [04:37:18] Obtained from https://github.com/tseemann/snippy [04:37:18] Detected operating system: linux [04:37:18] Enabling bundled linux tools. [04:37:18] Found bwa - /usr/local/bin/bwa [04:37:18] Found bcftools - /usr/local/bin/bcftools [04:37:18] Found samtools - /usr/local/bin/samtools [04:37:18] Found java - /usr/local/bin/java [04:37:18] Found snpEff - /usr/local/bin/snpEff [04:37:18] Found samclip - /usr/local/bin/samclip [04:37:18] Found seqtk - /usr/local/bin/seqtk [04:37:18] Found parallel - /usr/local/bin/parallel [04:37:18] Found freebayes - /usr/local/bin/freebayes [04:37:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:37:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:37:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:37:18] Found vcfuniq - /usr/local/bin/vcfuniq [04:37:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:37:18] Found gzip - /bin/gzip [04:37:18] Found vt - /usr/local/bin/vt [04:37:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:37:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:37:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:37:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:37:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:37:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:37:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:37:19] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:37:45] This is snippy 4.6.0
Show full stderr[04:37:45] This is snippy 4.6.0 [04:37:45] Written by Torsten Seemann [04:37:45] Obtained from https://github.com/tseemann/snippy [04:37:45] Detected operating system: linux [04:37:45] Enabling bundled linux tools. [04:37:45] Found bwa - /usr/local/bin/bwa [04:37:45] Found bcftools - /usr/local/bin/bcftools [04:37:45] Found samtools - /usr/local/bin/samtools [04:37:45] Found java - /usr/local/bin/java [04:37:45] Found snpEff - /usr/local/bin/snpEff [04:37:45] Found samclip - /usr/local/bin/samclip [04:37:45] Found seqtk - /usr/local/bin/seqtk [04:37:45] Found parallel - /usr/local/bin/parallel [04:37:45] Found freebayes - /usr/local/bin/freebayes [04:37:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:37:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:37:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:37:45] Found vcfuniq - /usr/local/bin/vcfuniq [04:37:45] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:37:45] Found gzip - /bin/gzip [04:37:45] Found vt - /usr/local/bin/vt [04:37:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:37:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:37:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:37:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:37:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:37:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:37:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:37:45] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:38:27] This is snippy 4.6.0
Show full stderr[04:38:27] This is snippy 4.6.0 [04:38:27] Written by Torsten Seemann [04:38:27] Obtained from https://github.com/tseemann/snippy [04:38:27] Detected operating system: linux [04:38:27] Enabling bundled linux tools. [04:38:27] Found bwa - /usr/local/bin/bwa [04:38:27] Found bcftools - /usr/local/bin/bcftools [04:38:27] Found samtools - /usr/local/bin/samtools [04:38:27] Found java - /usr/local/bin/java [04:38:27] Found snpEff - /usr/local/bin/snpEff [04:38:27] Found samclip - /usr/local/bin/samclip [04:38:27] Found seqtk - /usr/local/bin/seqtk [04:38:27] Found parallel - /usr/local/bin/parallel [04:38:27] Found freebayes - /usr/local/bin/freebayes [04:38:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:38:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:38:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:38:27] Found vcfuniq - /usr/local/bin/vcfuniq [04:38:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:38:27] Found gzip - /bin/gzip [04:38:27] Found vt - /usr/local/bin/vt [04:38:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:38:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:38:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:38:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:38:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:38:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:38:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:38:28] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:38:39] This is snippy 4.6.0
Show full stderr[04:38:39] This is snippy 4.6.0 [04:38:39] Written by Torsten Seemann [04:38:39] Obtained from https://github.com/tseemann/snippy [04:38:39] Detected operating system: linux [04:38:39] Enabling bundled linux tools. [04:38:39] Found bwa - /usr/local/bin/bwa [04:38:39] Found bcftools - /usr/local/bin/bcftools [04:38:39] Found samtools - /usr/local/bin/samtools [04:38:39] Found java - /usr/local/bin/java [04:38:39] Found snpEff - /usr/local/bin/snpEff [04:38:39] Found samclip - /usr/local/bin/samclip [04:38:39] Found seqtk - /usr/local/bin/seqtk [04:38:39] Found parallel - /usr/local/bin/parallel [04:38:39] Found freebayes - /usr/local/bin/freebayes [04:38:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:38:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:38:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:38:39] Found vcfuniq - /usr/local/bin/vcfuniq [04:38:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:38:39] Found gzip - /bin/gzip [04:38:39] Found vt - /usr/local/bin/vt [04:38:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:38:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:38:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:38:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:38:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:38:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:38:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:38:40] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:36:57] This is snippy 4.6.0
Show full stderr[04:36:57] This is snippy 4.6.0 [04:36:57] Written by Torsten Seemann [04:36:57] Obtained from https://github.com/tseemann/snippy [04:36:57] Detected operating system: linux [04:36:57] Enabling bundled linux tools. [04:36:57] Found bwa - /usr/local/bin/bwa [04:36:57] Found bcftools - /usr/local/bin/bcftools [04:36:57] Found samtools - /usr/local/bin/samtools [04:36:57] Found java - /usr/local/bin/java [04:36:57] Found snpEff - /usr/local/bin/snpEff [04:36:57] Found samclip - /usr/local/bin/samclip [04:36:57] Found seqtk - /usr/local/bin/seqtk [04:36:57] Found parallel - /usr/local/bin/parallel [04:36:57] Found freebayes - /usr/local/bin/freebayes [04:36:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:36:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:36:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:36:57] Found vcfuniq - /usr/local/bin/vcfuniq [04:36:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:36:57] Found gzip - /bin/gzip [04:36:57] Found vt - /usr/local/bin/vt [04:36:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:36:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:36:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:36:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:36:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:36:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:36:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:36:58] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:38:48] This is snippy 4.6.0
Show full stderr[04:38:48] This is snippy 4.6.0 [04:38:48] Written by Torsten Seemann [04:38:48] Obtained from https://github.com/tseemann/snippy [04:38:48] Detected operating system: linux [04:38:48] Enabling bundled linux tools. [04:38:48] Found bwa - /usr/local/bin/bwa [04:38:48] Found bcftools - /usr/local/bin/bcftools [04:38:48] Found samtools - /usr/local/bin/samtools [04:38:48] Found java - /usr/local/bin/java [04:38:48] Found snpEff - /usr/local/bin/snpEff [04:38:48] Found samclip - /usr/local/bin/samclip [04:38:48] Found seqtk - /usr/local/bin/seqtk [04:38:48] Found parallel - /usr/local/bin/parallel [04:38:48] Found freebayes - /usr/local/bin/freebayes [04:38:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:38:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:38:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:38:48] Found vcfuniq - /usr/local/bin/vcfuniq [04:38:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:38:48] Found gzip - /bin/gzip [04:38:48] Found vt - /usr/local/bin/vt [04:38:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:38:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:38:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:38:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:38:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:38:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:38:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:38:49] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:39:54] This is snippy 4.6.0
Show full stderr[04:39:54] This is snippy 4.6.0 [04:39:54] Written by Torsten Seemann [04:39:54] Obtained from https://github.com/tseemann/snippy [04:39:54] Detected operating system: linux [04:39:54] Enabling bundled linux tools. [04:39:54] Found bwa - /usr/local/bin/bwa [04:39:54] Found bcftools - /usr/local/bin/bcftools [04:39:54] Found samtools - /usr/local/bin/samtools [04:39:54] Found java - /usr/local/bin/java [04:39:54] Found snpEff - /usr/local/bin/snpEff [04:39:54] Found samclip - /usr/local/bin/samclip [04:39:54] Found seqtk - /usr/local/bin/seqtk [04:39:54] Found parallel - /usr/local/bin/parallel [04:39:54] Found freebayes - /usr/local/bin/freebayes [04:39:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:39:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:39:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:39:54] Found vcfuniq - /usr/local/bin/vcfuniq [04:39:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:39:54] Found gzip - /bin/gzip [04:39:54] Found vt - /usr/local/bin/vt [04:39:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:39:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:39:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:39:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:39:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:39:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:39:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:39:55] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:37:12] This is snippy 4.6.0
Show full stderr[04:37:12] This is snippy 4.6.0 [04:37:12] Written by Torsten Seemann [04:37:12] Obtained from https://github.com/tseemann/snippy [04:37:12] Detected operating system: linux [04:37:12] Enabling bundled linux tools. [04:37:12] Found bwa - /usr/local/bin/bwa [04:37:12] Found bcftools - /usr/local/bin/bcftools [04:37:12] Found samtools - /usr/local/bin/samtools [04:37:12] Found java - /usr/local/bin/java [04:37:12] Found snpEff - /usr/local/bin/snpEff [04:37:12] Found samclip - /usr/local/bin/samclip [04:37:12] Found seqtk - /usr/local/bin/seqtk [04:37:12] Found parallel - /usr/local/bin/parallel [04:37:12] Found freebayes - /usr/local/bin/freebayes [04:37:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:37:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:37:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:37:12] Found vcfuniq - /usr/local/bin/vcfuniq [04:37:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:37:12] Found gzip - /bin/gzip [04:37:12] Found vt - /usr/local/bin/vt [04:37:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:37:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:37:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:37:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:37:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:37:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:37:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:37:13] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:37:30] This is snippy 4.6.0
Show full stderr[04:37:30] This is snippy 4.6.0 [04:37:30] Written by Torsten Seemann [04:37:30] Obtained from https://github.com/tseemann/snippy [04:37:30] Detected operating system: linux [04:37:30] Enabling bundled linux tools. [04:37:30] Found bwa - /usr/local/bin/bwa [04:37:30] Found bcftools - /usr/local/bin/bcftools [04:37:30] Found samtools - /usr/local/bin/samtools [04:37:30] Found java - /usr/local/bin/java [04:37:30] Found snpEff - /usr/local/bin/snpEff [04:37:30] Found samclip - /usr/local/bin/samclip [04:37:30] Found seqtk - /usr/local/bin/seqtk [04:37:30] Found parallel - /usr/local/bin/parallel [04:37:30] Found freebayes - /usr/local/bin/freebayes [04:37:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:37:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:37:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:37:30] Found vcfuniq - /usr/local/bin/vcfuniq [04:37:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:37:30] Found gzip - /bin/gzip [04:37:30] Found vt - /usr/local/bin/vt [04:37:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:37:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:37:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:37:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:37:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:37:30] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:37:30] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:37:30] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:38:33] This is snippy 4.6.0
Show full stderr[04:38:33] This is snippy 4.6.0 [04:38:33] Written by Torsten Seemann [04:38:33] Obtained from https://github.com/tseemann/snippy [04:38:33] Detected operating system: linux [04:38:33] Enabling bundled linux tools. [04:38:33] Found bwa - /usr/local/bin/bwa [04:38:33] Found bcftools - /usr/local/bin/bcftools [04:38:33] Found samtools - /usr/local/bin/samtools [04:38:33] Found java - /usr/local/bin/java [04:38:33] Found snpEff - /usr/local/bin/snpEff [04:38:33] Found samclip - /usr/local/bin/samclip [04:38:33] Found seqtk - /usr/local/bin/seqtk [04:38:33] Found parallel - /usr/local/bin/parallel [04:38:33] Found freebayes - /usr/local/bin/freebayes [04:38:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:38:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:38:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:38:33] Found vcfuniq - /usr/local/bin/vcfuniq [04:38:33] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:38:33] Found gzip - /bin/gzip [04:38:33] Found vt - /usr/local/bin/vt [04:38:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:38:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:38:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:38:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:38:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:38:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:38:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:38:34] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:37:21] This is snippy 4.6.0
Show full stderr[04:37:21] This is snippy 4.6.0 [04:37:21] Written by Torsten Seemann [04:37:21] Obtained from https://github.com/tseemann/snippy [04:37:21] Detected operating system: linux [04:37:21] Enabling bundled linux tools. [04:37:21] Found bwa - /usr/local/bin/bwa [04:37:21] Found bcftools - /usr/local/bin/bcftools [04:37:21] Found samtools - /usr/local/bin/samtools [04:37:21] Found java - /usr/local/bin/java [04:37:21] Found snpEff - /usr/local/bin/snpEff [04:37:21] Found samclip - /usr/local/bin/samclip [04:37:21] Found seqtk - /usr/local/bin/seqtk [04:37:21] Found parallel - /usr/local/bin/parallel [04:37:21] Found freebayes - /usr/local/bin/freebayes [04:37:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:37:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:37:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:37:21] Found vcfuniq - /usr/local/bin/vcfuniq [04:37:21] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:37:21] Found gzip - /bin/gzip [04:37:21] Found vt - /usr/local/bin/vt [04:37:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:37:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:37:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:37:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:37:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:37:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:37:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:37:22] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:37:36] This is snippy 4.6.0
Show full stderr[04:37:36] This is snippy 4.6.0 [04:37:36] Written by Torsten Seemann [04:37:36] Obtained from https://github.com/tseemann/snippy [04:37:36] Detected operating system: linux [04:37:36] Enabling bundled linux tools. [04:37:36] Found bwa - /usr/local/bin/bwa [04:37:36] Found bcftools - /usr/local/bin/bcftools [04:37:36] Found samtools - /usr/local/bin/samtools [04:37:36] Found java - /usr/local/bin/java [04:37:36] Found snpEff - /usr/local/bin/snpEff [04:37:36] Found samclip - /usr/local/bin/samclip [04:37:36] Found seqtk - /usr/local/bin/seqtk [04:37:36] Found parallel - /usr/local/bin/parallel [04:37:36] Found freebayes - /usr/local/bin/freebayes [04:37:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:37:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:37:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:37:36] Found vcfuniq - /usr/local/bin/vcfuniq [04:37:36] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:37:36] Found gzip - /bin/gzip [04:37:36] Found vt - /usr/local/bin/vt [04:37:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:37:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:37:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:37:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:37:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:37:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:37:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:37:37] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:38:42] This is snippy 4.6.0
Show full stderr[04:38:42] This is snippy 4.6.0 [04:38:42] Written by Torsten Seemann [04:38:42] Obtained from https://github.com/tseemann/snippy [04:38:42] Detected operating system: linux [04:38:42] Enabling bundled linux tools. [04:38:42] Found bwa - /usr/local/bin/bwa [04:38:42] Found bcftools - /usr/local/bin/bcftools [04:38:42] Found samtools - /usr/local/bin/samtools [04:38:42] Found java - /usr/local/bin/java [04:38:42] Found snpEff - /usr/local/bin/snpEff [04:38:42] Found samclip - /usr/local/bin/samclip [04:38:42] Found seqtk - /usr/local/bin/seqtk [04:38:42] Found parallel - /usr/local/bin/parallel [04:38:42] Found freebayes - /usr/local/bin/freebayes [04:38:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:38:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:38:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:38:42] Found vcfuniq - /usr/local/bin/vcfuniq [04:38:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:38:42] Found gzip - /bin/gzip [04:38:42] Found vt - /usr/local/bin/vt [04:38:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:38:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:38:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:38:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:38:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:38:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:38:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:38:43] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:38:45] This is snippy 4.6.0
Show full stderr[04:38:45] This is snippy 4.6.0 [04:38:45] Written by Torsten Seemann [04:38:45] Obtained from https://github.com/tseemann/snippy [04:38:45] Detected operating system: linux [04:38:45] Enabling bundled linux tools. [04:38:45] Found bwa - /usr/local/bin/bwa [04:38:45] Found bcftools - /usr/local/bin/bcftools [04:38:45] Found samtools - /usr/local/bin/samtools [04:38:45] Found java - /usr/local/bin/java [04:38:45] Found snpEff - /usr/local/bin/snpEff [04:38:45] Found samclip - /usr/local/bin/samclip [04:38:45] Found seqtk - /usr/local/bin/seqtk [04:38:45] Found parallel - /usr/local/bin/parallel [04:38:45] Found freebayes - /usr/local/bin/freebayes [04:38:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:38:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:38:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:38:45] Found vcfuniq - /usr/local/bin/vcfuniq [04:38:45] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:38:45] Found gzip - /bin/gzip [04:38:45] Found vt - /usr/local/bin/vt [04:38:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:38:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:38:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:38:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:38:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:38:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:38:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:38:46] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:38:57] This is snippy 4.6.0
Show full stderr[04:38:57] This is snippy 4.6.0 [04:38:57] Written by Torsten Seemann [04:38:57] Obtained from https://github.com/tseemann/snippy [04:38:57] Detected operating system: linux [04:38:57] Enabling bundled linux tools. [04:38:57] Found bwa - /usr/local/bin/bwa [04:38:57] Found bcftools - /usr/local/bin/bcftools [04:38:57] Found samtools - /usr/local/bin/samtools [04:38:57] Found java - /usr/local/bin/java [04:38:57] Found snpEff - /usr/local/bin/snpEff [04:38:57] Found samclip - /usr/local/bin/samclip [04:38:57] Found seqtk - /usr/local/bin/seqtk [04:38:57] Found parallel - /usr/local/bin/parallel [04:38:57] Found freebayes - /usr/local/bin/freebayes [04:38:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:38:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:38:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:38:57] Found vcfuniq - /usr/local/bin/vcfuniq [04:38:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:38:57] Found gzip - /bin/gzip [04:38:57] Found vt - /usr/local/bin/vt [04:38:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:38:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:38:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:38:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:38:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:38:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:38:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:38:58] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:39:42] This is snippy 4.6.0
Show full stderr[04:39:42] This is snippy 4.6.0 [04:39:42] Written by Torsten Seemann [04:39:42] Obtained from https://github.com/tseemann/snippy [04:39:42] Detected operating system: linux [04:39:42] Enabling bundled linux tools. [04:39:42] Found bwa - /usr/local/bin/bwa [04:39:42] Found bcftools - /usr/local/bin/bcftools [04:39:42] Found samtools - /usr/local/bin/samtools [04:39:42] Found java - /usr/local/bin/java [04:39:42] Found snpEff - /usr/local/bin/snpEff [04:39:42] Found samclip - /usr/local/bin/samclip [04:39:42] Found seqtk - /usr/local/bin/seqtk [04:39:42] Found parallel - /usr/local/bin/parallel [04:39:42] Found freebayes - /usr/local/bin/freebayes [04:39:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:39:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:39:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:39:42] Found vcfuniq - /usr/local/bin/vcfuniq [04:39:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:39:42] Found gzip - /bin/gzip [04:39:42] Found vt - /usr/local/bin/vt [04:39:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:39:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:39:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:39:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:39:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:39:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:39:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:39:43] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:40:42] This is snippy 4.6.0
Show full stderr[04:40:42] This is snippy 4.6.0 [04:40:42] Written by Torsten Seemann [04:40:42] Obtained from https://github.com/tseemann/snippy [04:40:42] Detected operating system: linux [04:40:42] Enabling bundled linux tools. [04:40:42] Found bwa - /usr/local/bin/bwa [04:40:42] Found bcftools - /usr/local/bin/bcftools [04:40:42] Found samtools - /usr/local/bin/samtools [04:40:42] Found java - /usr/local/bin/java [04:40:42] Found snpEff - /usr/local/bin/snpEff [04:40:42] Found samclip - /usr/local/bin/samclip [04:40:42] Found seqtk - /usr/local/bin/seqtk [04:40:42] Found parallel - /usr/local/bin/parallel [04:40:42] Found freebayes - /usr/local/bin/freebayes [04:40:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:40:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:40:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:40:42] Found vcfuniq - /usr/local/bin/vcfuniq [04:40:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:40:42] Found gzip - /bin/gzip [04:40:42] Found vt - /usr/local/bin/vt [04:40:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:40:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:40:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:40:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:40:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:40:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:40:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:40:43] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:41:15] This is snippy 4.6.0
Show full stderr[04:41:15] This is snippy 4.6.0 [04:41:15] Written by Torsten Seemann [04:41:15] Obtained from https://github.com/tseemann/snippy [04:41:15] Detected operating system: linux [04:41:15] Enabling bundled linux tools. [04:41:15] Found bwa - /usr/local/bin/bwa [04:41:15] Found bcftools - /usr/local/bin/bcftools [04:41:15] Found samtools - /usr/local/bin/samtools [04:41:15] Found java - /usr/local/bin/java [04:41:15] Found snpEff - /usr/local/bin/snpEff [04:41:15] Found samclip - /usr/local/bin/samclip [04:41:15] Found seqtk - /usr/local/bin/seqtk [04:41:15] Found parallel - /usr/local/bin/parallel [04:41:15] Found freebayes - /usr/local/bin/freebayes [04:41:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:41:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:41:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:41:15] Found vcfuniq - /usr/local/bin/vcfuniq [04:41:15] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:41:15] Found gzip - /bin/gzip [04:41:15] Found vt - /usr/local/bin/vt [04:41:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:41:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:41:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:41:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:41:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:41:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:41:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:41:16] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:41:40] This is snippy 4.6.0
Show full stderr[04:41:40] This is snippy 4.6.0 [04:41:40] Written by Torsten Seemann [04:41:40] Obtained from https://github.com/tseemann/snippy [04:41:40] Detected operating system: linux [04:41:40] Enabling bundled linux tools. [04:41:40] Found bwa - /usr/local/bin/bwa [04:41:40] Found bcftools - /usr/local/bin/bcftools [04:41:40] Found samtools - /usr/local/bin/samtools [04:41:40] Found java - /usr/local/bin/java [04:41:40] Found snpEff - /usr/local/bin/snpEff [04:41:40] Found samclip - /usr/local/bin/samclip [04:41:40] Found seqtk - /usr/local/bin/seqtk [04:41:40] Found parallel - /usr/local/bin/parallel [04:41:40] Found freebayes - /usr/local/bin/freebayes [04:41:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:41:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:41:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:41:40] Found vcfuniq - /usr/local/bin/vcfuniq [04:41:40] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:41:40] Found gzip - /bin/gzip [04:41:40] Found vt - /usr/local/bin/vt [04:41:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:41:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:41:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:41:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:41:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:41:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:41:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:41:41] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:42:07] This is snippy 4.6.0
Show full stderr[04:42:07] This is snippy 4.6.0 [04:42:07] Written by Torsten Seemann [04:42:07] Obtained from https://github.com/tseemann/snippy [04:42:07] Detected operating system: linux [04:42:07] Enabling bundled linux tools. [04:42:07] Found bwa - /usr/local/bin/bwa [04:42:07] Found bcftools - /usr/local/bin/bcftools [04:42:07] Found samtools - /usr/local/bin/samtools [04:42:07] Found java - /usr/local/bin/java [04:42:07] Found snpEff - /usr/local/bin/snpEff [04:42:07] Found samclip - /usr/local/bin/samclip [04:42:07] Found seqtk - /usr/local/bin/seqtk [04:42:07] Found parallel - /usr/local/bin/parallel [04:42:07] Found freebayes - /usr/local/bin/freebayes [04:42:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:42:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:42:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:42:07] Found vcfuniq - /usr/local/bin/vcfuniq [04:42:07] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:42:07] Found gzip - /bin/gzip [04:42:07] Found vt - /usr/local/bin/vt [04:42:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:42:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:42:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:42:11] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:42:11] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:42:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:42:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:42:16] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:42:17] This is snippy 4.6.0
Show full stderr[04:42:17] This is snippy 4.6.0 [04:42:17] Written by Torsten Seemann [04:42:17] Obtained from https://github.com/tseemann/snippy [04:42:17] Detected operating system: linux [04:42:17] Enabling bundled linux tools. [04:42:17] Found bwa - /usr/local/bin/bwa [04:42:17] Found bcftools - /usr/local/bin/bcftools [04:42:17] Found samtools - /usr/local/bin/samtools [04:42:17] Found java - /usr/local/bin/java [04:42:17] Found snpEff - /usr/local/bin/snpEff [04:42:17] Found samclip - /usr/local/bin/samclip [04:42:17] Found seqtk - /usr/local/bin/seqtk [04:42:17] Found parallel - /usr/local/bin/parallel [04:42:17] Found freebayes - /usr/local/bin/freebayes [04:42:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:42:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:42:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:42:17] Found vcfuniq - /usr/local/bin/vcfuniq [04:42:17] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:42:17] Found gzip - /bin/gzip [04:42:17] Found vt - /usr/local/bin/vt [04:42:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:42:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:42:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:42:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:42:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:42:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:42:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:42:18] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:42:12] This is snippy 4.6.0
Show full stderr[04:42:12] This is snippy 4.6.0 [04:42:12] Written by Torsten Seemann [04:42:12] Obtained from https://github.com/tseemann/snippy [04:42:12] Detected operating system: linux [04:42:12] Enabling bundled linux tools. [04:42:12] Found bwa - /usr/local/bin/bwa [04:42:12] Found bcftools - /usr/local/bin/bcftools [04:42:12] Found samtools - /usr/local/bin/samtools [04:42:12] Found java - /usr/local/bin/java [04:42:12] Found snpEff - /usr/local/bin/snpEff [04:42:12] Found samclip - /usr/local/bin/samclip [04:42:12] Found seqtk - /usr/local/bin/seqtk [04:42:12] Found parallel - /usr/local/bin/parallel [04:42:12] Found freebayes - /usr/local/bin/freebayes [04:42:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:42:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:42:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:42:12] Found vcfuniq - /usr/local/bin/vcfuniq [04:42:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:42:12] Found gzip - /bin/gzip [04:42:12] Found vt - /usr/local/bin/vt [04:42:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:42:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:42:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:42:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:42:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:42:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:42:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:42:14] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:42:13] This is snippy 4.6.0
Show full stderr[04:42:13] This is snippy 4.6.0 [04:42:13] Written by Torsten Seemann [04:42:13] Obtained from https://github.com/tseemann/snippy [04:42:13] Detected operating system: linux [04:42:13] Enabling bundled linux tools. [04:42:13] Found bwa - /usr/local/bin/bwa [04:42:13] Found bcftools - /usr/local/bin/bcftools [04:42:13] Found samtools - /usr/local/bin/samtools [04:42:13] Found java - /usr/local/bin/java [04:42:13] Found snpEff - /usr/local/bin/snpEff [04:42:13] Found samclip - /usr/local/bin/samclip [04:42:13] Found seqtk - /usr/local/bin/seqtk [04:42:13] Found parallel - /usr/local/bin/parallel [04:42:13] Found freebayes - /usr/local/bin/freebayes [04:42:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:42:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:42:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:42:13] Found vcfuniq - /usr/local/bin/vcfuniq [04:42:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:42:13] Found gzip - /bin/gzip [04:42:13] Found vt - /usr/local/bin/vt [04:42:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:42:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:42:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:42:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:42:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:42:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:42:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:42:14] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:40:35] This is snippy 4.6.0
Show full stderr[04:40:35] This is snippy 4.6.0 [04:40:35] Written by Torsten Seemann [04:40:35] Obtained from https://github.com/tseemann/snippy [04:40:35] Detected operating system: linux [04:40:35] Enabling bundled linux tools. [04:40:35] Found bwa - /usr/local/bin/bwa [04:40:35] Found bcftools - /usr/local/bin/bcftools [04:40:35] Found samtools - /usr/local/bin/samtools [04:40:35] Found java - /usr/local/bin/java [04:40:35] Found snpEff - /usr/local/bin/snpEff [04:40:35] Found samclip - /usr/local/bin/samclip [04:40:35] Found seqtk - /usr/local/bin/seqtk [04:40:35] Found parallel - /usr/local/bin/parallel [04:40:35] Found freebayes - /usr/local/bin/freebayes [04:40:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:40:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:40:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:40:35] Found vcfuniq - /usr/local/bin/vcfuniq [04:40:35] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:40:35] Found gzip - /bin/gzip [04:40:35] Found vt - /usr/local/bin/vt [04:40:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:40:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:40:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:40:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:40:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:40:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:40:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:40:36] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:41:03] This is snippy 4.6.0
Show full stderr[04:41:03] This is snippy 4.6.0 [04:41:03] Written by Torsten Seemann [04:41:03] Obtained from https://github.com/tseemann/snippy [04:41:03] Detected operating system: linux [04:41:03] Enabling bundled linux tools. [04:41:03] Found bwa - /usr/local/bin/bwa [04:41:03] Found bcftools - /usr/local/bin/bcftools [04:41:03] Found samtools - /usr/local/bin/samtools [04:41:03] Found java - /usr/local/bin/java [04:41:03] Found snpEff - /usr/local/bin/snpEff [04:41:03] Found samclip - /usr/local/bin/samclip [04:41:03] Found seqtk - /usr/local/bin/seqtk [04:41:03] Found parallel - /usr/local/bin/parallel [04:41:03] Found freebayes - /usr/local/bin/freebayes [04:41:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:41:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:41:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:41:03] Found vcfuniq - /usr/local/bin/vcfuniq [04:41:03] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:41:03] Found gzip - /bin/gzip [04:41:03] Found vt - /usr/local/bin/vt [04:41:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:41:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:41:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:41:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:41:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:41:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:41:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:41:04] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:41:52] This is snippy 4.6.0
Show full stderr[04:41:52] This is snippy 4.6.0 [04:41:52] Written by Torsten Seemann [04:41:52] Obtained from https://github.com/tseemann/snippy [04:41:52] Detected operating system: linux [04:41:52] Enabling bundled linux tools. [04:41:52] Found bwa - /usr/local/bin/bwa [04:41:52] Found bcftools - /usr/local/bin/bcftools [04:41:52] Found samtools - /usr/local/bin/samtools [04:41:52] Found java - /usr/local/bin/java [04:41:52] Found snpEff - /usr/local/bin/snpEff [04:41:52] Found samclip - /usr/local/bin/samclip [04:41:52] Found seqtk - /usr/local/bin/seqtk [04:41:52] Found parallel - /usr/local/bin/parallel [04:41:52] Found freebayes - /usr/local/bin/freebayes [04:41:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:41:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:41:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:41:52] Found vcfuniq - /usr/local/bin/vcfuniq [04:41:52] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:41:52] Found gzip - /bin/gzip [04:41:52] Found vt - /usr/local/bin/vt [04:41:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:41:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:41:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:41:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:41:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:41:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:41:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:41:53] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:42:36] This is snippy 4.6.0
Show full stderr[04:42:36] This is snippy 4.6.0 [04:42:36] Written by Torsten Seemann [04:42:36] Obtained from https://github.com/tseemann/snippy [04:42:36] Detected operating system: linux [04:42:36] Enabling bundled linux tools. [04:42:36] Found bwa - /usr/local/bin/bwa [04:42:36] Found bcftools - /usr/local/bin/bcftools [04:42:36] Found samtools - /usr/local/bin/samtools [04:42:36] Found java - /usr/local/bin/java [04:42:36] Found snpEff - /usr/local/bin/snpEff [04:42:36] Found samclip - /usr/local/bin/samclip [04:42:36] Found seqtk - /usr/local/bin/seqtk [04:42:36] Found parallel - /usr/local/bin/parallel [04:42:36] Found freebayes - /usr/local/bin/freebayes [04:42:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:42:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:42:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:42:36] Found vcfuniq - /usr/local/bin/vcfuniq [04:42:36] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:42:36] Found gzip - /bin/gzip [04:42:36] Found vt - /usr/local/bin/vt [04:42:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:42:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:42:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:42:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:42:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:42:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:42:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:42:37] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:42:44] This is snippy 4.6.0
Show full stderr[04:42:44] This is snippy 4.6.0 [04:42:44] Written by Torsten Seemann [04:42:44] Obtained from https://github.com/tseemann/snippy [04:42:44] Detected operating system: linux [04:42:44] Enabling bundled linux tools. [04:42:44] Found bwa - /usr/local/bin/bwa [04:42:44] Found bcftools - /usr/local/bin/bcftools [04:42:44] Found samtools - /usr/local/bin/samtools [04:42:44] Found java - /usr/local/bin/java [04:42:44] Found snpEff - /usr/local/bin/snpEff [04:42:44] Found samclip - /usr/local/bin/samclip [04:42:44] Found seqtk - /usr/local/bin/seqtk [04:42:44] Found parallel - /usr/local/bin/parallel [04:42:44] Found freebayes - /usr/local/bin/freebayes [04:42:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:42:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:42:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:42:44] Found vcfuniq - /usr/local/bin/vcfuniq [04:42:44] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:42:44] Found gzip - /bin/gzip [04:42:44] Found vt - /usr/local/bin/vt [04:42:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:42:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:42:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:42:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:42:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:42:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:42:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:42:45] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:40:59] This is snippy 4.6.0
Show full stderr[04:40:59] This is snippy 4.6.0 [04:40:59] Written by Torsten Seemann [04:40:59] Obtained from https://github.com/tseemann/snippy [04:40:59] Detected operating system: linux [04:40:59] Enabling bundled linux tools. [04:40:59] Found bwa - /usr/local/bin/bwa [04:40:59] Found bcftools - /usr/local/bin/bcftools [04:40:59] Found samtools - /usr/local/bin/samtools [04:40:59] Found java - /usr/local/bin/java [04:40:59] Found snpEff - /usr/local/bin/snpEff [04:40:59] Found samclip - /usr/local/bin/samclip [04:40:59] Found seqtk - /usr/local/bin/seqtk [04:40:59] Found parallel - /usr/local/bin/parallel [04:40:59] Found freebayes - /usr/local/bin/freebayes [04:40:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:40:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:40:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:40:59] Found vcfuniq - /usr/local/bin/vcfuniq [04:40:59] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:40:59] Found gzip - /bin/gzip [04:40:59] Found vt - /usr/local/bin/vt [04:40:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:40:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:40:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:40:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:40:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:41:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:41:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:41:00] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:41:06] This is snippy 4.6.0
Show full stderr[04:41:06] This is snippy 4.6.0 [04:41:06] Written by Torsten Seemann [04:41:06] Obtained from https://github.com/tseemann/snippy [04:41:06] Detected operating system: linux [04:41:06] Enabling bundled linux tools. [04:41:06] Found bwa - /usr/local/bin/bwa [04:41:06] Found bcftools - /usr/local/bin/bcftools [04:41:06] Found samtools - /usr/local/bin/samtools [04:41:06] Found java - /usr/local/bin/java [04:41:06] Found snpEff - /usr/local/bin/snpEff [04:41:06] Found samclip - /usr/local/bin/samclip [04:41:06] Found seqtk - /usr/local/bin/seqtk [04:41:06] Found parallel - /usr/local/bin/parallel [04:41:06] Found freebayes - /usr/local/bin/freebayes [04:41:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:41:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:41:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:41:06] Found vcfuniq - /usr/local/bin/vcfuniq [04:41:06] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:41:06] Found gzip - /bin/gzip [04:41:06] Found vt - /usr/local/bin/vt [04:41:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:41:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:41:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:41:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:41:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:41:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:41:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:41:07] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:41:12] This is snippy 4.6.0
Show full stderr[04:41:12] This is snippy 4.6.0 [04:41:12] Written by Torsten Seemann [04:41:12] Obtained from https://github.com/tseemann/snippy [04:41:12] Detected operating system: linux [04:41:12] Enabling bundled linux tools. [04:41:12] Found bwa - /usr/local/bin/bwa [04:41:12] Found bcftools - /usr/local/bin/bcftools [04:41:12] Found samtools - /usr/local/bin/samtools [04:41:12] Found java - /usr/local/bin/java [04:41:12] Found snpEff - /usr/local/bin/snpEff [04:41:12] Found samclip - /usr/local/bin/samclip [04:41:12] Found seqtk - /usr/local/bin/seqtk [04:41:12] Found parallel - /usr/local/bin/parallel [04:41:12] Found freebayes - /usr/local/bin/freebayes [04:41:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:41:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:41:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:41:12] Found vcfuniq - /usr/local/bin/vcfuniq [04:41:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:41:12] Found gzip - /bin/gzip [04:41:12] Found vt - /usr/local/bin/vt [04:41:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:41:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:41:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:41:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:41:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:41:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:41:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:41:13] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:41:27] This is snippy 4.6.0
Show full stderr[04:41:27] This is snippy 4.6.0 [04:41:27] Written by Torsten Seemann [04:41:27] Obtained from https://github.com/tseemann/snippy [04:41:27] Detected operating system: linux [04:41:27] Enabling bundled linux tools. [04:41:27] Found bwa - /usr/local/bin/bwa [04:41:27] Found bcftools - /usr/local/bin/bcftools [04:41:27] Found samtools - /usr/local/bin/samtools [04:41:27] Found java - /usr/local/bin/java [04:41:27] Found snpEff - /usr/local/bin/snpEff [04:41:27] Found samclip - /usr/local/bin/samclip [04:41:27] Found seqtk - /usr/local/bin/seqtk [04:41:27] Found parallel - /usr/local/bin/parallel [04:41:27] Found freebayes - /usr/local/bin/freebayes [04:41:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:41:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:41:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:41:27] Found vcfuniq - /usr/local/bin/vcfuniq [04:41:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:41:27] Found gzip - /bin/gzip [04:41:27] Found vt - /usr/local/bin/vt [04:41:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:41:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:41:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:41:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:41:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:41:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:41:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:41:28] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:42:39] This is snippy 4.6.0
Show full stderr[04:42:39] This is snippy 4.6.0 [04:42:39] Written by Torsten Seemann [04:42:39] Obtained from https://github.com/tseemann/snippy [04:42:39] Detected operating system: linux [04:42:39] Enabling bundled linux tools. [04:42:39] Found bwa - /usr/local/bin/bwa [04:42:39] Found bcftools - /usr/local/bin/bcftools [04:42:39] Found samtools - /usr/local/bin/samtools [04:42:39] Found java - /usr/local/bin/java [04:42:40] Found snpEff - /usr/local/bin/snpEff [04:42:40] Found samclip - /usr/local/bin/samclip [04:42:40] Found seqtk - /usr/local/bin/seqtk [04:42:40] Found parallel - /usr/local/bin/parallel [04:42:40] Found freebayes - /usr/local/bin/freebayes [04:42:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:42:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:42:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:42:40] Found vcfuniq - /usr/local/bin/vcfuniq [04:42:40] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:42:40] Found gzip - /bin/gzip [04:42:40] Found vt - /usr/local/bin/vt [04:42:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:42:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:42:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:42:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:42:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:42:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:42:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:42:41] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:43:00] This is snippy 4.6.0
Show full stderr[04:43:00] This is snippy 4.6.0 [04:43:00] Written by Torsten Seemann [04:43:00] Obtained from https://github.com/tseemann/snippy [04:43:00] Detected operating system: linux [04:43:00] Enabling bundled linux tools. [04:43:00] Found bwa - /usr/local/bin/bwa [04:43:00] Found bcftools - /usr/local/bin/bcftools [04:43:00] Found samtools - /usr/local/bin/samtools [04:43:00] Found java - /usr/local/bin/java [04:43:00] Found snpEff - /usr/local/bin/snpEff [04:43:00] Found samclip - /usr/local/bin/samclip [04:43:00] Found seqtk - /usr/local/bin/seqtk [04:43:00] Found parallel - /usr/local/bin/parallel [04:43:00] Found freebayes - /usr/local/bin/freebayes [04:43:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:43:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:43:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:43:00] Found vcfuniq - /usr/local/bin/vcfuniq [04:43:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:43:00] Found gzip - /bin/gzip [04:43:00] Found vt - /usr/local/bin/vt [04:43:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:43:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:43:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:43:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:43:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:43:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:43:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:43:01] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:43:34] This is snippy 4.6.0
Show full stderr[04:43:34] This is snippy 4.6.0 [04:43:34] Written by Torsten Seemann [04:43:34] Obtained from https://github.com/tseemann/snippy [04:43:34] Detected operating system: linux [04:43:34] Enabling bundled linux tools. [04:43:34] Found bwa - /usr/local/bin/bwa [04:43:34] Found bcftools - /usr/local/bin/bcftools [04:43:34] Found samtools - /usr/local/bin/samtools [04:43:34] Found java - /usr/local/bin/java [04:43:34] Found snpEff - /usr/local/bin/snpEff [04:43:34] Found samclip - /usr/local/bin/samclip [04:43:34] Found seqtk - /usr/local/bin/seqtk [04:43:34] Found parallel - /usr/local/bin/parallel [04:43:34] Found freebayes - /usr/local/bin/freebayes [04:43:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:43:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:43:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:43:34] Found vcfuniq - /usr/local/bin/vcfuniq [04:43:34] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:43:34] Found gzip - /bin/gzip [04:43:34] Found vt - /usr/local/bin/vt [04:43:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:43:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:43:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:43:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:43:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:43:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:43:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:43:35] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:44:12] This is snippy 4.6.0
Show full stderr[04:44:12] This is snippy 4.6.0 [04:44:12] Written by Torsten Seemann [04:44:12] Obtained from https://github.com/tseemann/snippy [04:44:12] Detected operating system: linux [04:44:12] Enabling bundled linux tools. [04:44:12] Found bwa - /usr/local/bin/bwa [04:44:12] Found bcftools - /usr/local/bin/bcftools [04:44:12] Found samtools - /usr/local/bin/samtools [04:44:12] Found java - /usr/local/bin/java [04:44:12] Found snpEff - /usr/local/bin/snpEff [04:44:12] Found samclip - /usr/local/bin/samclip [04:44:12] Found seqtk - /usr/local/bin/seqtk [04:44:12] Found parallel - /usr/local/bin/parallel [04:44:12] Found freebayes - /usr/local/bin/freebayes [04:44:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:44:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:44:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:44:12] Found vcfuniq - /usr/local/bin/vcfuniq [04:44:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:44:12] Found gzip - /bin/gzip [04:44:12] Found vt - /usr/local/bin/vt [04:44:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:44:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:44:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:44:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:44:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:44:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:44:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:44:13] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:44:16] This is snippy 4.6.0
Show full stderr[04:44:16] This is snippy 4.6.0 [04:44:16] Written by Torsten Seemann [04:44:16] Obtained from https://github.com/tseemann/snippy [04:44:16] Detected operating system: linux [04:44:16] Enabling bundled linux tools. [04:44:16] Found bwa - /usr/local/bin/bwa [04:44:16] Found bcftools - /usr/local/bin/bcftools [04:44:16] Found samtools - /usr/local/bin/samtools [04:44:16] Found java - /usr/local/bin/java [04:44:16] Found snpEff - /usr/local/bin/snpEff [04:44:16] Found samclip - /usr/local/bin/samclip [04:44:16] Found seqtk - /usr/local/bin/seqtk [04:44:16] Found parallel - /usr/local/bin/parallel [04:44:16] Found freebayes - /usr/local/bin/freebayes [04:44:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:44:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:44:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:44:16] Found vcfuniq - /usr/local/bin/vcfuniq [04:44:16] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:44:16] Found gzip - /bin/gzip [04:44:16] Found vt - /usr/local/bin/vt [04:44:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:44:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:44:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:44:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:44:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:44:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:44:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:44:17] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:44:28] This is snippy 4.6.0
Show full stderr[04:44:28] This is snippy 4.6.0 [04:44:28] Written by Torsten Seemann [04:44:28] Obtained from https://github.com/tseemann/snippy [04:44:28] Detected operating system: linux [04:44:28] Enabling bundled linux tools. [04:44:28] Found bwa - /usr/local/bin/bwa [04:44:28] Found bcftools - /usr/local/bin/bcftools [04:44:28] Found samtools - /usr/local/bin/samtools [04:44:28] Found java - /usr/local/bin/java [04:44:28] Found snpEff - /usr/local/bin/snpEff [04:44:28] Found samclip - /usr/local/bin/samclip [04:44:28] Found seqtk - /usr/local/bin/seqtk [04:44:28] Found parallel - /usr/local/bin/parallel [04:44:28] Found freebayes - /usr/local/bin/freebayes [04:44:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:44:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:44:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:44:28] Found vcfuniq - /usr/local/bin/vcfuniq [04:44:28] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:44:28] Found gzip - /bin/gzip [04:44:28] Found vt - /usr/local/bin/vt [04:44:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:44:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:44:29] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:44:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:44:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:44:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:44:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:44:29] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:44:49] This is snippy 4.6.0
Show full stderr[04:44:49] This is snippy 4.6.0 [04:44:49] Written by Torsten Seemann [04:44:49] Obtained from https://github.com/tseemann/snippy [04:44:49] Detected operating system: linux [04:44:49] Enabling bundled linux tools. [04:44:49] Found bwa - /usr/local/bin/bwa [04:44:49] Found bcftools - /usr/local/bin/bcftools [04:44:49] Found samtools - /usr/local/bin/samtools [04:44:49] Found java - /usr/local/bin/java [04:44:49] Found snpEff - /usr/local/bin/snpEff [04:44:49] Found samclip - /usr/local/bin/samclip [04:44:49] Found seqtk - /usr/local/bin/seqtk [04:44:49] Found parallel - /usr/local/bin/parallel [04:44:49] Found freebayes - /usr/local/bin/freebayes [04:44:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:44:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:44:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:44:49] Found vcfuniq - /usr/local/bin/vcfuniq [04:44:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:44:49] Found gzip - /bin/gzip [04:44:49] Found vt - /usr/local/bin/vt [04:44:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:44:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:44:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:44:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:44:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:44:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:44:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:44:50] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:43:12] This is snippy 4.6.0
Show full stderr[04:43:12] This is snippy 4.6.0 [04:43:12] Written by Torsten Seemann [04:43:12] Obtained from https://github.com/tseemann/snippy [04:43:12] Detected operating system: linux [04:43:12] Enabling bundled linux tools. [04:43:12] Found bwa - /usr/local/bin/bwa [04:43:12] Found bcftools - /usr/local/bin/bcftools [04:43:12] Found samtools - /usr/local/bin/samtools [04:43:12] Found java - /usr/local/bin/java [04:43:12] Found snpEff - /usr/local/bin/snpEff [04:43:12] Found samclip - /usr/local/bin/samclip [04:43:12] Found seqtk - /usr/local/bin/seqtk [04:43:12] Found parallel - /usr/local/bin/parallel [04:43:12] Found freebayes - /usr/local/bin/freebayes [04:43:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:43:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:43:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:43:12] Found vcfuniq - /usr/local/bin/vcfuniq [04:43:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:43:12] Found gzip - /bin/gzip [04:43:12] Found vt - /usr/local/bin/vt [04:43:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:43:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:43:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:43:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:43:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:43:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:43:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:43:13] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:43:18] This is snippy 4.6.0
Show full stderr[04:43:18] This is snippy 4.6.0 [04:43:18] Written by Torsten Seemann [04:43:18] Obtained from https://github.com/tseemann/snippy [04:43:18] Detected operating system: linux [04:43:18] Enabling bundled linux tools. [04:43:18] Found bwa - /usr/local/bin/bwa [04:43:18] Found bcftools - /usr/local/bin/bcftools [04:43:18] Found samtools - /usr/local/bin/samtools [04:43:18] Found java - /usr/local/bin/java [04:43:18] Found snpEff - /usr/local/bin/snpEff [04:43:18] Found samclip - /usr/local/bin/samclip [04:43:18] Found seqtk - /usr/local/bin/seqtk [04:43:18] Found parallel - /usr/local/bin/parallel [04:43:18] Found freebayes - /usr/local/bin/freebayes [04:43:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:43:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:43:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:43:18] Found vcfuniq - /usr/local/bin/vcfuniq [04:43:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:43:18] Found gzip - /bin/gzip [04:43:18] Found vt - /usr/local/bin/vt [04:43:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:43:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:43:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:43:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:43:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:43:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:43:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:43:20] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:43:27] This is snippy 4.6.0
Show full stderr[04:43:27] This is snippy 4.6.0 [04:43:27] Written by Torsten Seemann [04:43:27] Obtained from https://github.com/tseemann/snippy [04:43:27] Detected operating system: linux [04:43:27] Enabling bundled linux tools. [04:43:27] Found bwa - /usr/local/bin/bwa [04:43:27] Found bcftools - /usr/local/bin/bcftools [04:43:27] Found samtools - /usr/local/bin/samtools [04:43:27] Found java - /usr/local/bin/java [04:43:27] Found snpEff - /usr/local/bin/snpEff [04:43:27] Found samclip - /usr/local/bin/samclip [04:43:27] Found seqtk - /usr/local/bin/seqtk [04:43:27] Found parallel - /usr/local/bin/parallel [04:43:27] Found freebayes - /usr/local/bin/freebayes [04:43:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:43:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:43:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:43:27] Found vcfuniq - /usr/local/bin/vcfuniq [04:43:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:43:27] Found gzip - /bin/gzip [04:43:27] Found vt - /usr/local/bin/vt [04:43:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:43:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:43:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:43:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:43:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:43:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:43:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:43:29] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:43:58] This is snippy 4.6.0
Show full stderr[04:43:58] This is snippy 4.6.0 [04:43:58] Written by Torsten Seemann [04:43:58] Obtained from https://github.com/tseemann/snippy [04:43:58] Detected operating system: linux [04:43:58] Enabling bundled linux tools. [04:43:58] Found bwa - /usr/local/bin/bwa [04:43:58] Found bcftools - /usr/local/bin/bcftools [04:43:58] Found samtools - /usr/local/bin/samtools [04:43:58] Found java - /usr/local/bin/java [04:43:58] Found snpEff - /usr/local/bin/snpEff [04:43:58] Found samclip - /usr/local/bin/samclip [04:43:58] Found seqtk - /usr/local/bin/seqtk [04:43:58] Found parallel - /usr/local/bin/parallel [04:43:58] Found freebayes - /usr/local/bin/freebayes [04:43:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:43:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:43:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:43:58] Found vcfuniq - /usr/local/bin/vcfuniq [04:43:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:43:58] Found gzip - /bin/gzip [04:43:58] Found vt - /usr/local/bin/vt [04:43:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:43:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:43:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:43:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:43:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:43:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:43:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:43:59] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:42:18] This is snippy 4.6.0
Show full stderr[04:42:18] This is snippy 4.6.0 [04:42:18] Written by Torsten Seemann [04:42:18] Obtained from https://github.com/tseemann/snippy [04:42:18] Detected operating system: linux [04:42:18] Enabling bundled linux tools. [04:42:18] Found bwa - /usr/local/bin/bwa [04:42:18] Found bcftools - /usr/local/bin/bcftools [04:42:18] Found samtools - /usr/local/bin/samtools [04:42:18] Found java - /usr/local/bin/java [04:42:18] Found snpEff - /usr/local/bin/snpEff [04:42:18] Found samclip - /usr/local/bin/samclip [04:42:18] Found seqtk - /usr/local/bin/seqtk [04:42:18] Found parallel - /usr/local/bin/parallel [04:42:18] Found freebayes - /usr/local/bin/freebayes [04:42:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:42:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:42:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:42:18] Found vcfuniq - /usr/local/bin/vcfuniq [04:42:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:42:18] Found gzip - /bin/gzip [04:42:18] Found vt - /usr/local/bin/vt [04:42:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:42:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:42:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:42:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:42:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:42:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:42:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:42:19] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:55:06] This is snippy 4.6.0
Show full stderr[04:55:06] This is snippy 4.6.0 [04:55:06] Written by Torsten Seemann [04:55:06] Obtained from https://github.com/tseemann/snippy [04:55:06] Detected operating system: linux [04:55:06] Enabling bundled linux tools. [04:55:06] Found bwa - /usr/local/bin/bwa [04:55:06] Found bcftools - /usr/local/bin/bcftools [04:55:06] Found samtools - /usr/local/bin/samtools [04:55:06] Found java - /usr/local/bin/java [04:55:06] Found snpEff - /usr/local/bin/snpEff [04:55:06] Found samclip - /usr/local/bin/samclip [04:55:06] Found seqtk - /usr/local/bin/seqtk [04:55:06] Found parallel - /usr/local/bin/parallel [04:55:06] Found freebayes - /usr/local/bin/freebayes [04:55:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:55:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:55:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:55:06] Found vcfuniq - /usr/local/bin/vcfuniq [04:55:06] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:55:06] Found gzip - /bin/gzip [04:55:06] Found vt - /usr/local/bin/vt [04:55:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:55:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:55:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:55:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:55:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:55:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:55:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:55:08] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:55:21] This is snippy 4.6.0
Show full stderr[04:55:21] This is snippy 4.6.0 [04:55:21] Written by Torsten Seemann [04:55:21] Obtained from https://github.com/tseemann/snippy [04:55:21] Detected operating system: linux [04:55:21] Enabling bundled linux tools. [04:55:21] Found bwa - /usr/local/bin/bwa [04:55:21] Found bcftools - /usr/local/bin/bcftools [04:55:21] Found samtools - /usr/local/bin/samtools [04:55:21] Found java - /usr/local/bin/java [04:55:21] Found snpEff - /usr/local/bin/snpEff [04:55:21] Found samclip - /usr/local/bin/samclip [04:55:21] Found seqtk - /usr/local/bin/seqtk [04:55:21] Found parallel - /usr/local/bin/parallel [04:55:21] Found freebayes - /usr/local/bin/freebayes [04:55:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:55:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:55:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:55:21] Found vcfuniq - /usr/local/bin/vcfuniq [04:55:21] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:55:21] Found gzip - /bin/gzip [04:55:21] Found vt - /usr/local/bin/vt [04:55:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:55:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:55:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:55:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:55:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:55:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:55:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:55:22] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:55:27] This is snippy 4.6.0
Show full stderr[04:55:27] This is snippy 4.6.0 [04:55:27] Written by Torsten Seemann [04:55:27] Obtained from https://github.com/tseemann/snippy [04:55:27] Detected operating system: linux [04:55:27] Enabling bundled linux tools. [04:55:27] Found bwa - /usr/local/bin/bwa [04:55:27] Found bcftools - /usr/local/bin/bcftools [04:55:27] Found samtools - /usr/local/bin/samtools [04:55:27] Found java - /usr/local/bin/java [04:55:27] Found snpEff - /usr/local/bin/snpEff [04:55:27] Found samclip - /usr/local/bin/samclip [04:55:27] Found seqtk - /usr/local/bin/seqtk [04:55:27] Found parallel - /usr/local/bin/parallel [04:55:27] Found freebayes - /usr/local/bin/freebayes [04:55:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:55:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:55:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:55:27] Found vcfuniq - /usr/local/bin/vcfuniq [04:55:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:55:27] Found gzip - /bin/gzip [04:55:27] Found vt - /usr/local/bin/vt [04:55:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:55:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:55:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:55:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:55:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:55:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:55:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:55:29] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:55:36] This is snippy 4.6.0
Show full stderr[04:55:36] This is snippy 4.6.0 [04:55:36] Written by Torsten Seemann [04:55:36] Obtained from https://github.com/tseemann/snippy [04:55:36] Detected operating system: linux [04:55:36] Enabling bundled linux tools. [04:55:36] Found bwa - /usr/local/bin/bwa [04:55:36] Found bcftools - /usr/local/bin/bcftools [04:55:36] Found samtools - /usr/local/bin/samtools [04:55:36] Found java - /usr/local/bin/java [04:55:36] Found snpEff - /usr/local/bin/snpEff [04:55:36] Found samclip - /usr/local/bin/samclip [04:55:36] Found seqtk - /usr/local/bin/seqtk [04:55:36] Found parallel - /usr/local/bin/parallel [04:55:36] Found freebayes - /usr/local/bin/freebayes [04:55:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:55:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:55:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:55:36] Found vcfuniq - /usr/local/bin/vcfuniq [04:55:36] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:55:36] Found gzip - /bin/gzip [04:55:36] Found vt - /usr/local/bin/vt [04:55:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:55:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:55:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:55:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:55:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:55:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:55:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:55:37] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:55:43] This is snippy 4.6.0
Show full stderr[04:55:43] This is snippy 4.6.0 [04:55:43] Written by Torsten Seemann [04:55:43] Obtained from https://github.com/tseemann/snippy [04:55:43] Detected operating system: linux [04:55:43] Enabling bundled linux tools. [04:55:43] Found bwa - /usr/local/bin/bwa [04:55:43] Found bcftools - /usr/local/bin/bcftools [04:55:43] Found samtools - /usr/local/bin/samtools [04:55:43] Found java - /usr/local/bin/java [04:55:43] Found snpEff - /usr/local/bin/snpEff [04:55:43] Found samclip - /usr/local/bin/samclip [04:55:43] Found seqtk - /usr/local/bin/seqtk [04:55:43] Found parallel - /usr/local/bin/parallel [04:55:43] Found freebayes - /usr/local/bin/freebayes [04:55:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:55:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:55:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:55:43] Found vcfuniq - /usr/local/bin/vcfuniq [04:55:43] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:55:43] Found gzip - /bin/gzip [04:55:43] Found vt - /usr/local/bin/vt [04:55:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:55:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:55:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:55:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:55:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:55:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:55:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:55:44] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:56:18] This is snippy 4.6.0
Show full stderr[04:56:18] This is snippy 4.6.0 [04:56:18] Written by Torsten Seemann [04:56:18] Obtained from https://github.com/tseemann/snippy [04:56:18] Detected operating system: linux [04:56:18] Enabling bundled linux tools. [04:56:18] Found bwa - /usr/local/bin/bwa [04:56:18] Found bcftools - /usr/local/bin/bcftools [04:56:18] Found samtools - /usr/local/bin/samtools [04:56:18] Found java - /usr/local/bin/java [04:56:18] Found snpEff - /usr/local/bin/snpEff [04:56:18] Found samclip - /usr/local/bin/samclip [04:56:18] Found seqtk - /usr/local/bin/seqtk [04:56:18] Found parallel - /usr/local/bin/parallel [04:56:18] Found freebayes - /usr/local/bin/freebayes [04:56:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:56:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:56:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:56:18] Found vcfuniq - /usr/local/bin/vcfuniq [04:56:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:56:18] Found gzip - /bin/gzip [04:56:18] Found vt - /usr/local/bin/vt [04:56:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:56:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:56:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:56:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:56:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:56:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:56:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:56:19] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:54:59] This is snippy 4.6.0
Show full stderr[04:54:59] This is snippy 4.6.0 [04:54:59] Written by Torsten Seemann [04:54:59] Obtained from https://github.com/tseemann/snippy [04:54:59] Detected operating system: linux [04:54:59] Enabling bundled linux tools. [04:54:59] Found bwa - /usr/local/bin/bwa [04:54:59] Found bcftools - /usr/local/bin/bcftools [04:54:59] Found samtools - /usr/local/bin/samtools [04:54:59] Found java - /usr/local/bin/java [04:54:59] Found snpEff - /usr/local/bin/snpEff [04:54:59] Found samclip - /usr/local/bin/samclip [04:54:59] Found seqtk - /usr/local/bin/seqtk [04:54:59] Found parallel - /usr/local/bin/parallel [04:54:59] Found freebayes - /usr/local/bin/freebayes [04:54:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:54:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:54:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:54:59] Found vcfuniq - /usr/local/bin/vcfuniq [04:54:59] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:54:59] Found gzip - /bin/gzip [04:54:59] Found vt - /usr/local/bin/vt [04:54:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:54:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:55:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:55:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:55:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:55:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:55:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:55:03] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:55:24] This is snippy 4.6.0
Show full stderr[04:55:24] This is snippy 4.6.0 [04:55:24] Written by Torsten Seemann [04:55:24] Obtained from https://github.com/tseemann/snippy [04:55:24] Detected operating system: linux [04:55:24] Enabling bundled linux tools. [04:55:24] Found bwa - /usr/local/bin/bwa [04:55:24] Found bcftools - /usr/local/bin/bcftools [04:55:24] Found samtools - /usr/local/bin/samtools [04:55:24] Found java - /usr/local/bin/java [04:55:24] Found snpEff - /usr/local/bin/snpEff [04:55:24] Found samclip - /usr/local/bin/samclip [04:55:24] Found seqtk - /usr/local/bin/seqtk [04:55:24] Found parallel - /usr/local/bin/parallel [04:55:24] Found freebayes - /usr/local/bin/freebayes [04:55:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:55:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:55:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:55:24] Found vcfuniq - /usr/local/bin/vcfuniq [04:55:24] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:55:24] Found gzip - /bin/gzip [04:55:24] Found vt - /usr/local/bin/vt [04:55:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:55:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:55:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:55:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:55:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:55:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:55:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:55:26] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:56:03] This is snippy 4.6.0
Show full stderr[04:56:03] This is snippy 4.6.0 [04:56:03] Written by Torsten Seemann [04:56:03] Obtained from https://github.com/tseemann/snippy [04:56:03] Detected operating system: linux [04:56:03] Enabling bundled linux tools. [04:56:03] Found bwa - /usr/local/bin/bwa [04:56:03] Found bcftools - /usr/local/bin/bcftools [04:56:03] Found samtools - /usr/local/bin/samtools [04:56:03] Found java - /usr/local/bin/java [04:56:03] Found snpEff - /usr/local/bin/snpEff [04:56:03] Found samclip - /usr/local/bin/samclip [04:56:03] Found seqtk - /usr/local/bin/seqtk [04:56:03] Found parallel - /usr/local/bin/parallel [04:56:03] Found freebayes - /usr/local/bin/freebayes [04:56:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:56:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:56:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:56:03] Found vcfuniq - /usr/local/bin/vcfuniq [04:56:03] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:56:03] Found gzip - /bin/gzip [04:56:03] Found vt - /usr/local/bin/vt [04:56:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:56:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:56:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:56:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:56:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:56:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:56:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:56:04] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:56:06] This is snippy 4.6.0
Show full stderr[04:56:06] This is snippy 4.6.0 [04:56:06] Written by Torsten Seemann [04:56:06] Obtained from https://github.com/tseemann/snippy [04:56:06] Detected operating system: linux [04:56:06] Enabling bundled linux tools. [04:56:06] Found bwa - /usr/local/bin/bwa [04:56:06] Found bcftools - /usr/local/bin/bcftools [04:56:06] Found samtools - /usr/local/bin/samtools [04:56:06] Found java - /usr/local/bin/java [04:56:06] Found snpEff - /usr/local/bin/snpEff [04:56:06] Found samclip - /usr/local/bin/samclip [04:56:06] Found seqtk - /usr/local/bin/seqtk [04:56:06] Found parallel - /usr/local/bin/parallel [04:56:06] Found freebayes - /usr/local/bin/freebayes [04:56:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:56:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:56:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:56:06] Found vcfuniq - /usr/local/bin/vcfuniq [04:56:06] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:56:06] Found gzip - /bin/gzip [04:56:06] Found vt - /usr/local/bin/vt [04:56:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:56:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:56:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:56:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:56:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:56:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:56:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:56:07] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:56:24] This is snippy 4.6.0
Show full stderr[04:56:24] This is snippy 4.6.0 [04:56:24] Written by Torsten Seemann [04:56:24] Obtained from https://github.com/tseemann/snippy [04:56:24] Detected operating system: linux [04:56:24] Enabling bundled linux tools. [04:56:24] Found bwa - /usr/local/bin/bwa [04:56:24] Found bcftools - /usr/local/bin/bcftools [04:56:24] Found samtools - /usr/local/bin/samtools [04:56:24] Found java - /usr/local/bin/java [04:56:24] Found snpEff - /usr/local/bin/snpEff [04:56:24] Found samclip - /usr/local/bin/samclip [04:56:24] Found seqtk - /usr/local/bin/seqtk [04:56:24] Found parallel - /usr/local/bin/parallel [04:56:24] Found freebayes - /usr/local/bin/freebayes [04:56:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:56:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:56:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:56:24] Found vcfuniq - /usr/local/bin/vcfuniq [04:56:24] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:56:24] Found gzip - /bin/gzip [04:56:24] Found vt - /usr/local/bin/vt [04:56:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:56:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:56:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:56:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:56:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:56:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:56:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:56:26] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:57:57] This is snippy 4.6.0
Show full stderr[04:57:57] This is snippy 4.6.0 [04:57:57] Written by Torsten Seemann [04:57:57] Obtained from https://github.com/tseemann/snippy [04:57:57] Detected operating system: linux [04:57:57] Enabling bundled linux tools. [04:57:57] Found bwa - /usr/local/bin/bwa [04:57:57] Found bcftools - /usr/local/bin/bcftools [04:57:57] Found samtools - /usr/local/bin/samtools [04:57:57] Found java - /usr/local/bin/java [04:57:57] Found snpEff - /usr/local/bin/snpEff [04:57:57] Found samclip - /usr/local/bin/samclip [04:57:57] Found seqtk - /usr/local/bin/seqtk [04:57:57] Found parallel - /usr/local/bin/parallel [04:57:57] Found freebayes - /usr/local/bin/freebayes [04:57:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:57:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:57:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:57:57] Found vcfuniq - /usr/local/bin/vcfuniq [04:57:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:57:57] Found gzip - /bin/gzip [04:57:57] Found vt - /usr/local/bin/vt [04:57:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:57:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:57:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:57:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:57:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:57:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:57:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:57:58] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:57:12] This is snippy 4.6.0
Show full stderr[04:57:12] This is snippy 4.6.0 [04:57:12] Written by Torsten Seemann [04:57:12] Obtained from https://github.com/tseemann/snippy [04:57:12] Detected operating system: linux [04:57:12] Enabling bundled linux tools. [04:57:12] Found bwa - /usr/local/bin/bwa [04:57:12] Found bcftools - /usr/local/bin/bcftools [04:57:12] Found samtools - /usr/local/bin/samtools [04:57:12] Found java - /usr/local/bin/java [04:57:12] Found snpEff - /usr/local/bin/snpEff [04:57:12] Found samclip - /usr/local/bin/samclip [04:57:12] Found seqtk - /usr/local/bin/seqtk [04:57:12] Found parallel - /usr/local/bin/parallel [04:57:12] Found freebayes - /usr/local/bin/freebayes [04:57:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:57:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:57:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:57:12] Found vcfuniq - /usr/local/bin/vcfuniq [04:57:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:57:12] Found gzip - /bin/gzip [04:57:12] Found vt - /usr/local/bin/vt [04:57:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:57:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:57:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:57:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:57:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:57:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:57:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:57:13] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:59:00] This is snippy 4.6.0
Show full stderr[04:59:00] This is snippy 4.6.0 [04:59:00] Written by Torsten Seemann [04:59:00] Obtained from https://github.com/tseemann/snippy [04:59:00] Detected operating system: linux [04:59:00] Enabling bundled linux tools. [04:59:00] Found bwa - /usr/local/bin/bwa [04:59:00] Found bcftools - /usr/local/bin/bcftools [04:59:00] Found samtools - /usr/local/bin/samtools [04:59:00] Found java - /usr/local/bin/java [04:59:00] Found snpEff - /usr/local/bin/snpEff [04:59:00] Found samclip - /usr/local/bin/samclip [04:59:00] Found seqtk - /usr/local/bin/seqtk [04:59:00] Found parallel - /usr/local/bin/parallel [04:59:00] Found freebayes - /usr/local/bin/freebayes [04:59:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:59:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:59:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:59:00] Found vcfuniq - /usr/local/bin/vcfuniq [04:59:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:59:00] Found gzip - /bin/gzip [04:59:00] Found vt - /usr/local/bin/vt [04:59:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:59:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:59:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:59:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:59:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:59:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:59:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:59:01] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:59:21] This is snippy 4.6.0
Show full stderr[04:59:21] This is snippy 4.6.0 [04:59:21] Written by Torsten Seemann [04:59:21] Obtained from https://github.com/tseemann/snippy [04:59:21] Detected operating system: linux [04:59:21] Enabling bundled linux tools. [04:59:21] Found bwa - /usr/local/bin/bwa [04:59:21] Found bcftools - /usr/local/bin/bcftools [04:59:21] Found samtools - /usr/local/bin/samtools [04:59:21] Found java - /usr/local/bin/java [04:59:21] Found snpEff - /usr/local/bin/snpEff [04:59:21] Found samclip - /usr/local/bin/samclip [04:59:21] Found seqtk - /usr/local/bin/seqtk [04:59:21] Found parallel - /usr/local/bin/parallel [04:59:21] Found freebayes - /usr/local/bin/freebayes [04:59:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:59:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:59:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:59:21] Found vcfuniq - /usr/local/bin/vcfuniq [04:59:21] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:59:21] Found gzip - /bin/gzip [04:59:21] Found vt - /usr/local/bin/vt [04:59:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:59:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:59:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:59:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:59:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:59:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:59:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:59:22] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:57:15] This is snippy 4.6.0
Show full stderr[04:57:15] This is snippy 4.6.0 [04:57:15] Written by Torsten Seemann [04:57:15] Obtained from https://github.com/tseemann/snippy [04:57:15] Detected operating system: linux [04:57:15] Enabling bundled linux tools. [04:57:15] Found bwa - /usr/local/bin/bwa [04:57:15] Found bcftools - /usr/local/bin/bcftools [04:57:15] Found samtools - /usr/local/bin/samtools [04:57:15] Found java - /usr/local/bin/java [04:57:15] Found snpEff - /usr/local/bin/snpEff [04:57:15] Found samclip - /usr/local/bin/samclip [04:57:15] Found seqtk - /usr/local/bin/seqtk [04:57:15] Found parallel - /usr/local/bin/parallel [04:57:15] Found freebayes - /usr/local/bin/freebayes [04:57:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:57:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:57:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:57:15] Found vcfuniq - /usr/local/bin/vcfuniq [04:57:15] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:57:15] Found gzip - /bin/gzip [04:57:15] Found vt - /usr/local/bin/vt [04:57:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:57:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:57:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:57:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:57:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:57:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:57:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:57:16] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:57:27] This is snippy 4.6.0
Show full stderr[04:57:27] This is snippy 4.6.0 [04:57:27] Written by Torsten Seemann [04:57:27] Obtained from https://github.com/tseemann/snippy [04:57:27] Detected operating system: linux [04:57:27] Enabling bundled linux tools. [04:57:27] Found bwa - /usr/local/bin/bwa [04:57:27] Found bcftools - /usr/local/bin/bcftools [04:57:27] Found samtools - /usr/local/bin/samtools [04:57:27] Found java - /usr/local/bin/java [04:57:27] Found snpEff - /usr/local/bin/snpEff [04:57:27] Found samclip - /usr/local/bin/samclip [04:57:27] Found seqtk - /usr/local/bin/seqtk [04:57:27] Found parallel - /usr/local/bin/parallel [04:57:27] Found freebayes - /usr/local/bin/freebayes [04:57:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:57:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:57:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:57:27] Found vcfuniq - /usr/local/bin/vcfuniq [04:57:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:57:27] Found gzip - /bin/gzip [04:57:27] Found vt - /usr/local/bin/vt [04:57:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:57:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:57:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:57:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:57:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:57:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:57:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:57:28] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:57:42] This is snippy 4.6.0
Show full stderr[04:57:42] This is snippy 4.6.0 [04:57:42] Written by Torsten Seemann [04:57:42] Obtained from https://github.com/tseemann/snippy [04:57:42] Detected operating system: linux [04:57:42] Enabling bundled linux tools. [04:57:42] Found bwa - /usr/local/bin/bwa [04:57:42] Found bcftools - /usr/local/bin/bcftools [04:57:42] Found samtools - /usr/local/bin/samtools [04:57:42] Found java - /usr/local/bin/java [04:57:42] Found snpEff - /usr/local/bin/snpEff [04:57:42] Found samclip - /usr/local/bin/samclip [04:57:42] Found seqtk - /usr/local/bin/seqtk [04:57:42] Found parallel - /usr/local/bin/parallel [04:57:42] Found freebayes - /usr/local/bin/freebayes [04:57:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:57:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:57:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:57:42] Found vcfuniq - /usr/local/bin/vcfuniq [04:57:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:57:42] Found gzip - /bin/gzip [04:57:42] Found vt - /usr/local/bin/vt [04:57:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:57:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:57:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:57:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:57:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:57:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:57:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:57:43] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:58:36] This is snippy 4.6.0
Show full stderr[04:58:36] This is snippy 4.6.0 [04:58:36] Written by Torsten Seemann [04:58:36] Obtained from https://github.com/tseemann/snippy [04:58:36] Detected operating system: linux [04:58:36] Enabling bundled linux tools. [04:58:36] Found bwa - /usr/local/bin/bwa [04:58:36] Found bcftools - /usr/local/bin/bcftools [04:58:36] Found samtools - /usr/local/bin/samtools [04:58:36] Found java - /usr/local/bin/java [04:58:36] Found snpEff - /usr/local/bin/snpEff [04:58:36] Found samclip - /usr/local/bin/samclip [04:58:36] Found seqtk - /usr/local/bin/seqtk [04:58:36] Found parallel - /usr/local/bin/parallel [04:58:36] Found freebayes - /usr/local/bin/freebayes [04:58:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:58:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:58:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:58:36] Found vcfuniq - /usr/local/bin/vcfuniq [04:58:36] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:58:36] Found gzip - /bin/gzip [04:58:36] Found vt - /usr/local/bin/vt [04:58:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:58:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:58:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:58:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:58:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:58:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:58:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:58:37] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:59:36] This is snippy 4.6.0
Show full stderr[04:59:36] This is snippy 4.6.0 [04:59:36] Written by Torsten Seemann [04:59:36] Obtained from https://github.com/tseemann/snippy [04:59:36] Detected operating system: linux [04:59:36] Enabling bundled linux tools. [04:59:36] Found bwa - /usr/local/bin/bwa [04:59:36] Found bcftools - /usr/local/bin/bcftools [04:59:36] Found samtools - /usr/local/bin/samtools [04:59:36] Found java - /usr/local/bin/java [04:59:37] Found snpEff - /usr/local/bin/snpEff [04:59:37] Found samclip - /usr/local/bin/samclip [04:59:37] Found seqtk - /usr/local/bin/seqtk [04:59:37] Found parallel - /usr/local/bin/parallel [04:59:37] Found freebayes - /usr/local/bin/freebayes [04:59:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:59:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:59:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:59:37] Found vcfuniq - /usr/local/bin/vcfuniq [04:59:37] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:59:37] Found gzip - /bin/gzip [04:59:37] Found vt - /usr/local/bin/vt [04:59:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:59:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:59:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:59:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:59:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:59:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:59:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:59:38] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:00:06] This is snippy 4.6.0
Show full stderr[05:00:06] This is snippy 4.6.0 [05:00:06] Written by Torsten Seemann [05:00:06] Obtained from https://github.com/tseemann/snippy [05:00:06] Detected operating system: linux [05:00:06] Enabling bundled linux tools. [05:00:06] Found bwa - /usr/local/bin/bwa [05:00:06] Found bcftools - /usr/local/bin/bcftools [05:00:06] Found samtools - /usr/local/bin/samtools [05:00:06] Found java - /usr/local/bin/java [05:00:06] Found snpEff - /usr/local/bin/snpEff [05:00:06] Found samclip - /usr/local/bin/samclip [05:00:06] Found seqtk - /usr/local/bin/seqtk [05:00:06] Found parallel - /usr/local/bin/parallel [05:00:06] Found freebayes - /usr/local/bin/freebayes [05:00:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:00:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:00:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:00:06] Found vcfuniq - /usr/local/bin/vcfuniq [05:00:06] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:00:06] Found gzip - /bin/gzip [05:00:06] Found vt - /usr/local/bin/vt [05:00:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:00:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:00:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:00:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:00:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:00:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:00:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:00:07] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:00:09] This is snippy 4.6.0
Show full stderr[05:00:09] This is snippy 4.6.0 [05:00:09] Written by Torsten Seemann [05:00:09] Obtained from https://github.com/tseemann/snippy [05:00:09] Detected operating system: linux [05:00:09] Enabling bundled linux tools. [05:00:09] Found bwa - /usr/local/bin/bwa [05:00:09] Found bcftools - /usr/local/bin/bcftools [05:00:09] Found samtools - /usr/local/bin/samtools [05:00:09] Found java - /usr/local/bin/java [05:00:09] Found snpEff - /usr/local/bin/snpEff [05:00:09] Found samclip - /usr/local/bin/samclip [05:00:09] Found seqtk - /usr/local/bin/seqtk [05:00:09] Found parallel - /usr/local/bin/parallel [05:00:09] Found freebayes - /usr/local/bin/freebayes [05:00:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:00:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:00:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:00:09] Found vcfuniq - /usr/local/bin/vcfuniq [05:00:09] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:00:09] Found gzip - /bin/gzip [05:00:09] Found vt - /usr/local/bin/vt [05:00:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:00:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:00:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:00:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:00:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:00:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:00:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:00:10] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:01:05] This is snippy 4.6.0
Show full stderr[05:01:05] This is snippy 4.6.0 [05:01:05] Written by Torsten Seemann [05:01:05] Obtained from https://github.com/tseemann/snippy [05:01:05] Detected operating system: linux [05:01:05] Enabling bundled linux tools. [05:01:05] Found bwa - /usr/local/bin/bwa [05:01:05] Found bcftools - /usr/local/bin/bcftools [05:01:05] Found samtools - /usr/local/bin/samtools [05:01:05] Found java - /usr/local/bin/java [05:01:05] Found snpEff - /usr/local/bin/snpEff [05:01:05] Found samclip - /usr/local/bin/samclip [05:01:05] Found seqtk - /usr/local/bin/seqtk [05:01:05] Found parallel - /usr/local/bin/parallel [05:01:05] Found freebayes - /usr/local/bin/freebayes [05:01:05] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:01:05] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:01:05] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:01:05] Found vcfuniq - /usr/local/bin/vcfuniq [05:01:05] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:01:05] Found gzip - /bin/gzip [05:01:06] Found vt - /usr/local/bin/vt [05:01:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:01:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:01:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:01:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:01:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:01:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:01:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:01:06] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:01:16] This is snippy 4.6.0
Show full stderr[05:01:16] This is snippy 4.6.0 [05:01:16] Written by Torsten Seemann [05:01:16] Obtained from https://github.com/tseemann/snippy [05:01:16] Detected operating system: linux [05:01:16] Enabling bundled linux tools. [05:01:16] Found bwa - /usr/local/bin/bwa [05:01:16] Found bcftools - /usr/local/bin/bcftools [05:01:16] Found samtools - /usr/local/bin/samtools [05:01:16] Found java - /usr/local/bin/java [05:01:16] Found snpEff - /usr/local/bin/snpEff [05:01:16] Found samclip - /usr/local/bin/samclip [05:01:16] Found seqtk - /usr/local/bin/seqtk [05:01:16] Found parallel - /usr/local/bin/parallel [05:01:16] Found freebayes - /usr/local/bin/freebayes [05:01:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:01:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:01:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:01:16] Found vcfuniq - /usr/local/bin/vcfuniq [05:01:16] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:01:16] Found gzip - /bin/gzip [05:01:16] Found vt - /usr/local/bin/vt [05:01:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:01:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:01:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:01:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:01:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:01:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:01:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:01:17] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:56:36] This is snippy 4.6.0
Show full stderr[04:56:36] This is snippy 4.6.0 [04:56:36] Written by Torsten Seemann [04:56:36] Obtained from https://github.com/tseemann/snippy [04:56:36] Detected operating system: linux [04:56:36] Enabling bundled linux tools. [04:56:36] Found bwa - /usr/local/bin/bwa [04:56:36] Found bcftools - /usr/local/bin/bcftools [04:56:36] Found samtools - /usr/local/bin/samtools [04:56:36] Found java - /usr/local/bin/java [04:56:36] Found snpEff - /usr/local/bin/snpEff [04:56:36] Found samclip - /usr/local/bin/samclip [04:56:36] Found seqtk - /usr/local/bin/seqtk [04:56:36] Found parallel - /usr/local/bin/parallel [04:56:36] Found freebayes - /usr/local/bin/freebayes [04:56:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:56:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:56:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:56:36] Found vcfuniq - /usr/local/bin/vcfuniq [04:56:36] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:56:36] Found gzip - /bin/gzip [04:56:36] Found vt - /usr/local/bin/vt [04:56:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:56:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:56:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:56:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:56:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:56:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:56:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:56:37] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:58:30] This is snippy 4.6.0
Show full stderr[04:58:30] This is snippy 4.6.0 [04:58:30] Written by Torsten Seemann [04:58:30] Obtained from https://github.com/tseemann/snippy [04:58:30] Detected operating system: linux [04:58:30] Enabling bundled linux tools. [04:58:30] Found bwa - /usr/local/bin/bwa [04:58:30] Found bcftools - /usr/local/bin/bcftools [04:58:30] Found samtools - /usr/local/bin/samtools [04:58:30] Found java - /usr/local/bin/java [04:58:30] Found snpEff - /usr/local/bin/snpEff [04:58:30] Found samclip - /usr/local/bin/samclip [04:58:30] Found seqtk - /usr/local/bin/seqtk [04:58:30] Found parallel - /usr/local/bin/parallel [04:58:30] Found freebayes - /usr/local/bin/freebayes [04:58:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:58:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:58:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:58:30] Found vcfuniq - /usr/local/bin/vcfuniq [04:58:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:58:30] Found gzip - /bin/gzip [04:58:30] Found vt - /usr/local/bin/vt [04:58:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:58:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:58:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:58:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:58:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:58:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:58:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:58:31] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:00:18] This is snippy 4.6.0
Show full stderr[05:00:18] This is snippy 4.6.0 [05:00:18] Written by Torsten Seemann [05:00:18] Obtained from https://github.com/tseemann/snippy [05:00:18] Detected operating system: linux [05:00:18] Enabling bundled linux tools. [05:00:18] Found bwa - /usr/local/bin/bwa [05:00:18] Found bcftools - /usr/local/bin/bcftools [05:00:18] Found samtools - /usr/local/bin/samtools [05:00:18] Found java - /usr/local/bin/java [05:00:18] Found snpEff - /usr/local/bin/snpEff [05:00:18] Found samclip - /usr/local/bin/samclip [05:00:18] Found seqtk - /usr/local/bin/seqtk [05:00:18] Found parallel - /usr/local/bin/parallel [05:00:18] Found freebayes - /usr/local/bin/freebayes [05:00:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:00:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:00:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:00:18] Found vcfuniq - /usr/local/bin/vcfuniq [05:00:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:00:18] Found gzip - /bin/gzip [05:00:18] Found vt - /usr/local/bin/vt [05:00:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:00:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:00:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:00:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:00:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:00:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:00:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:00:19] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:00:20] This is snippy 4.6.0
Show full stderr[05:00:20] This is snippy 4.6.0 [05:00:20] Written by Torsten Seemann [05:00:20] Obtained from https://github.com/tseemann/snippy [05:00:20] Detected operating system: linux [05:00:20] Enabling bundled linux tools. [05:00:20] Found bwa - /usr/local/bin/bwa [05:00:20] Found bcftools - /usr/local/bin/bcftools [05:00:20] Found samtools - /usr/local/bin/samtools [05:00:20] Found java - /usr/local/bin/java [05:00:20] Found snpEff - /usr/local/bin/snpEff [05:00:20] Found samclip - /usr/local/bin/samclip [05:00:20] Found seqtk - /usr/local/bin/seqtk [05:00:20] Found parallel - /usr/local/bin/parallel [05:00:20] Found freebayes - /usr/local/bin/freebayes [05:00:20] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:00:20] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:00:20] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:00:20] Found vcfuniq - /usr/local/bin/vcfuniq [05:00:20] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:00:20] Found gzip - /bin/gzip [05:00:20] Found vt - /usr/local/bin/vt [05:00:20] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:00:20] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:00:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:00:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:00:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:00:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:00:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:00:21] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:00:33] This is snippy 4.6.0
Show full stderr[05:00:33] This is snippy 4.6.0 [05:00:33] Written by Torsten Seemann [05:00:33] Obtained from https://github.com/tseemann/snippy [05:00:33] Detected operating system: linux [05:00:33] Enabling bundled linux tools. [05:00:33] Found bwa - /usr/local/bin/bwa [05:00:33] Found bcftools - /usr/local/bin/bcftools [05:00:33] Found samtools - /usr/local/bin/samtools [05:00:33] Found java - /usr/local/bin/java [05:00:33] Found snpEff - /usr/local/bin/snpEff [05:00:33] Found samclip - /usr/local/bin/samclip [05:00:33] Found seqtk - /usr/local/bin/seqtk [05:00:33] Found parallel - /usr/local/bin/parallel [05:00:33] Found freebayes - /usr/local/bin/freebayes [05:00:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:00:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:00:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:00:33] Found vcfuniq - /usr/local/bin/vcfuniq [05:00:33] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:00:33] Found gzip - /bin/gzip [05:00:33] Found vt - /usr/local/bin/vt [05:00:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:00:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:00:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:00:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:00:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:00:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:00:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:00:34] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:01:02] This is snippy 4.6.0
Show full stderr[05:01:02] This is snippy 4.6.0 [05:01:02] Written by Torsten Seemann [05:01:02] Obtained from https://github.com/tseemann/snippy [05:01:02] Detected operating system: linux [05:01:02] Enabling bundled linux tools. [05:01:02] Found bwa - /usr/local/bin/bwa [05:01:02] Found bcftools - /usr/local/bin/bcftools [05:01:02] Found samtools - /usr/local/bin/samtools [05:01:02] Found java - /usr/local/bin/java [05:01:02] Found snpEff - /usr/local/bin/snpEff [05:01:02] Found samclip - /usr/local/bin/samclip [05:01:02] Found seqtk - /usr/local/bin/seqtk [05:01:02] Found parallel - /usr/local/bin/parallel [05:01:02] Found freebayes - /usr/local/bin/freebayes [05:01:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:01:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:01:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:01:02] Found vcfuniq - /usr/local/bin/vcfuniq [05:01:02] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:01:02] Found gzip - /bin/gzip [05:01:02] Found vt - /usr/local/bin/vt [05:01:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:01:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:01:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:01:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:01:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:01:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:01:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:01:03] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:01:18] This is snippy 4.6.0
Show full stderr[05:01:18] This is snippy 4.6.0 [05:01:18] Written by Torsten Seemann [05:01:18] Obtained from https://github.com/tseemann/snippy [05:01:18] Detected operating system: linux [05:01:18] Enabling bundled linux tools. [05:01:18] Found bwa - /usr/local/bin/bwa [05:01:18] Found bcftools - /usr/local/bin/bcftools [05:01:18] Found samtools - /usr/local/bin/samtools [05:01:19] Found java - /usr/local/bin/java [05:01:19] Found snpEff - /usr/local/bin/snpEff [05:01:19] Found samclip - /usr/local/bin/samclip [05:01:19] Found seqtk - /usr/local/bin/seqtk [05:01:19] Found parallel - /usr/local/bin/parallel [05:01:19] Found freebayes - /usr/local/bin/freebayes [05:01:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:01:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:01:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:01:19] Found vcfuniq - /usr/local/bin/vcfuniq [05:01:19] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:01:19] Found gzip - /bin/gzip [05:01:19] Found vt - /usr/local/bin/vt [05:01:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:01:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:01:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:01:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:01:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:01:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:01:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:01:19] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:01:27] This is snippy 4.6.0
Show full stderr[05:01:27] This is snippy 4.6.0 [05:01:27] Written by Torsten Seemann [05:01:27] Obtained from https://github.com/tseemann/snippy [05:01:27] Detected operating system: linux [05:01:27] Enabling bundled linux tools. [05:01:27] Found bwa - /usr/local/bin/bwa [05:01:27] Found bcftools - /usr/local/bin/bcftools [05:01:27] Found samtools - /usr/local/bin/samtools [05:01:27] Found java - /usr/local/bin/java [05:01:27] Found snpEff - /usr/local/bin/snpEff [05:01:27] Found samclip - /usr/local/bin/samclip [05:01:27] Found seqtk - /usr/local/bin/seqtk [05:01:27] Found parallel - /usr/local/bin/parallel [05:01:27] Found freebayes - /usr/local/bin/freebayes [05:01:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:01:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:01:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:01:27] Found vcfuniq - /usr/local/bin/vcfuniq [05:01:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:01:27] Found gzip - /bin/gzip [05:01:27] Found vt - /usr/local/bin/vt [05:01:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:01:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:01:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:01:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:01:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:01:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:01:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:01:28] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:01:42] This is snippy 4.6.0
Show full stderr[05:01:42] This is snippy 4.6.0 [05:01:42] Written by Torsten Seemann [05:01:42] Obtained from https://github.com/tseemann/snippy [05:01:42] Detected operating system: linux [05:01:42] Enabling bundled linux tools. [05:01:42] Found bwa - /usr/local/bin/bwa [05:01:42] Found bcftools - /usr/local/bin/bcftools [05:01:42] Found samtools - /usr/local/bin/samtools [05:01:42] Found java - /usr/local/bin/java [05:01:42] Found snpEff - /usr/local/bin/snpEff [05:01:42] Found samclip - /usr/local/bin/samclip [05:01:42] Found seqtk - /usr/local/bin/seqtk [05:01:42] Found parallel - /usr/local/bin/parallel [05:01:42] Found freebayes - /usr/local/bin/freebayes [05:01:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:01:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:01:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:01:42] Found vcfuniq - /usr/local/bin/vcfuniq [05:01:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:01:42] Found gzip - /bin/gzip [05:01:42] Found vt - /usr/local/bin/vt [05:01:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:01:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:01:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:01:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:01:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:01:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:01:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:01:43] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:01:43] This is snippy 4.6.0
Show full stderr[05:01:43] This is snippy 4.6.0 [05:01:43] Written by Torsten Seemann [05:01:43] Obtained from https://github.com/tseemann/snippy [05:01:43] Detected operating system: linux [05:01:43] Enabling bundled linux tools. [05:01:43] Found bwa - /usr/local/bin/bwa [05:01:44] Found bcftools - /usr/local/bin/bcftools [05:01:44] Found samtools - /usr/local/bin/samtools [05:01:44] Found java - /usr/local/bin/java [05:01:44] Found snpEff - /usr/local/bin/snpEff [05:01:44] Found samclip - /usr/local/bin/samclip [05:01:44] Found seqtk - /usr/local/bin/seqtk [05:01:44] Found parallel - /usr/local/bin/parallel [05:01:44] Found freebayes - /usr/local/bin/freebayes [05:01:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:01:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:01:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:01:44] Found vcfuniq - /usr/local/bin/vcfuniq [05:01:44] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:01:44] Found gzip - /bin/gzip [05:01:44] Found vt - /usr/local/bin/vt [05:01:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:01:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:01:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:01:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:01:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:01:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:01:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:01:44] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:01:55] This is snippy 4.6.0
Show full stderr[05:01:55] This is snippy 4.6.0 [05:01:55] Written by Torsten Seemann [05:01:55] Obtained from https://github.com/tseemann/snippy [05:01:55] Detected operating system: linux [05:01:55] Enabling bundled linux tools. [05:01:55] Found bwa - /usr/local/bin/bwa [05:01:55] Found bcftools - /usr/local/bin/bcftools [05:01:55] Found samtools - /usr/local/bin/samtools [05:01:55] Found java - /usr/local/bin/java [05:01:55] Found snpEff - /usr/local/bin/snpEff [05:01:55] Found samclip - /usr/local/bin/samclip [05:01:55] Found seqtk - /usr/local/bin/seqtk [05:01:55] Found parallel - /usr/local/bin/parallel [05:01:55] Found freebayes - /usr/local/bin/freebayes [05:01:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:01:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:01:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:01:55] Found vcfuniq - /usr/local/bin/vcfuniq [05:01:56] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:01:56] Found gzip - /bin/gzip [05:01:56] Found vt - /usr/local/bin/vt [05:01:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:01:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:01:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:01:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:01:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:01:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:01:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:01:56] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:02:12] This is snippy 4.6.0
Show full stderr[05:02:12] This is snippy 4.6.0 [05:02:12] Written by Torsten Seemann [05:02:12] Obtained from https://github.com/tseemann/snippy [05:02:12] Detected operating system: linux [05:02:12] Enabling bundled linux tools. [05:02:12] Found bwa - /usr/local/bin/bwa [05:02:12] Found bcftools - /usr/local/bin/bcftools [05:02:12] Found samtools - /usr/local/bin/samtools [05:02:12] Found java - /usr/local/bin/java [05:02:12] Found snpEff - /usr/local/bin/snpEff [05:02:12] Found samclip - /usr/local/bin/samclip [05:02:12] Found seqtk - /usr/local/bin/seqtk [05:02:12] Found parallel - /usr/local/bin/parallel [05:02:12] Found freebayes - /usr/local/bin/freebayes [05:02:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:02:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:02:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:02:12] Found vcfuniq - /usr/local/bin/vcfuniq [05:02:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:02:13] Found gzip - /bin/gzip [05:02:13] Found vt - /usr/local/bin/vt [05:02:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:02:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:02:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:02:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:02:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:02:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:02:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:02:13] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:01:46] This is snippy 4.6.0
Show full stderr[05:01:46] This is snippy 4.6.0 [05:01:46] Written by Torsten Seemann [05:01:46] Obtained from https://github.com/tseemann/snippy [05:01:46] Detected operating system: linux [05:01:46] Enabling bundled linux tools. [05:01:46] Found bwa - /usr/local/bin/bwa [05:01:46] Found bcftools - /usr/local/bin/bcftools [05:01:46] Found samtools - /usr/local/bin/samtools [05:01:46] Found java - /usr/local/bin/java [05:01:46] Found snpEff - /usr/local/bin/snpEff [05:01:46] Found samclip - /usr/local/bin/samclip [05:01:46] Found seqtk - /usr/local/bin/seqtk [05:01:46] Found parallel - /usr/local/bin/parallel [05:01:46] Found freebayes - /usr/local/bin/freebayes [05:01:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:01:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:01:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:01:47] Found vcfuniq - /usr/local/bin/vcfuniq [05:01:47] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:01:47] Found gzip - /bin/gzip [05:01:47] Found vt - /usr/local/bin/vt [05:01:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:01:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:01:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:01:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:01:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:01:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:01:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:01:47] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:58:45] This is snippy 4.6.0
Show full stderr[04:58:45] This is snippy 4.6.0 [04:58:45] Written by Torsten Seemann [04:58:45] Obtained from https://github.com/tseemann/snippy [04:58:45] Detected operating system: linux [04:58:45] Enabling bundled linux tools. [04:58:45] Found bwa - /usr/local/bin/bwa [04:58:45] Found bcftools - /usr/local/bin/bcftools [04:58:45] Found samtools - /usr/local/bin/samtools [04:58:45] Found java - /usr/local/bin/java [04:58:45] Found snpEff - /usr/local/bin/snpEff [04:58:45] Found samclip - /usr/local/bin/samclip [04:58:45] Found seqtk - /usr/local/bin/seqtk [04:58:45] Found parallel - /usr/local/bin/parallel [04:58:45] Found freebayes - /usr/local/bin/freebayes [04:58:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:58:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:58:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:58:45] Found vcfuniq - /usr/local/bin/vcfuniq [04:58:45] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:58:45] Found gzip - /bin/gzip [04:58:45] Found vt - /usr/local/bin/vt [04:58:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:58:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:58:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:58:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:58:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:58:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:58:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:58:46] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:59:15] This is snippy 4.6.0
Show full stderr[04:59:15] This is snippy 4.6.0 [04:59:15] Written by Torsten Seemann [04:59:15] Obtained from https://github.com/tseemann/snippy [04:59:15] Detected operating system: linux [04:59:15] Enabling bundled linux tools. [04:59:15] Found bwa - /usr/local/bin/bwa [04:59:15] Found bcftools - /usr/local/bin/bcftools [04:59:15] Found samtools - /usr/local/bin/samtools [04:59:15] Found java - /usr/local/bin/java [04:59:15] Found snpEff - /usr/local/bin/snpEff [04:59:15] Found samclip - /usr/local/bin/samclip [04:59:15] Found seqtk - /usr/local/bin/seqtk [04:59:15] Found parallel - /usr/local/bin/parallel [04:59:15] Found freebayes - /usr/local/bin/freebayes [04:59:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:59:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:59:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:59:15] Found vcfuniq - /usr/local/bin/vcfuniq [04:59:15] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:59:15] Found gzip - /bin/gzip [04:59:15] Found vt - /usr/local/bin/vt [04:59:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:59:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:59:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:59:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:59:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:59:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:59:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:59:16] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:59:27] This is snippy 4.6.0
Show full stderr[04:59:27] This is snippy 4.6.0 [04:59:27] Written by Torsten Seemann [04:59:27] Obtained from https://github.com/tseemann/snippy [04:59:27] Detected operating system: linux [04:59:27] Enabling bundled linux tools. [04:59:27] Found bwa - /usr/local/bin/bwa [04:59:27] Found bcftools - /usr/local/bin/bcftools [04:59:27] Found samtools - /usr/local/bin/samtools [04:59:27] Found java - /usr/local/bin/java [04:59:27] Found snpEff - /usr/local/bin/snpEff [04:59:27] Found samclip - /usr/local/bin/samclip [04:59:27] Found seqtk - /usr/local/bin/seqtk [04:59:27] Found parallel - /usr/local/bin/parallel [04:59:27] Found freebayes - /usr/local/bin/freebayes [04:59:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:59:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:59:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:59:27] Found vcfuniq - /usr/local/bin/vcfuniq [04:59:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:59:27] Found gzip - /bin/gzip [04:59:27] Found vt - /usr/local/bin/vt [04:59:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:59:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:59:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:59:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:59:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:59:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:59:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:59:28] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:59:30] This is snippy 4.6.0
Show full stderr[04:59:30] This is snippy 4.6.0 [04:59:30] Written by Torsten Seemann [04:59:30] Obtained from https://github.com/tseemann/snippy [04:59:30] Detected operating system: linux [04:59:30] Enabling bundled linux tools. [04:59:30] Found bwa - /usr/local/bin/bwa [04:59:30] Found bcftools - /usr/local/bin/bcftools [04:59:30] Found samtools - /usr/local/bin/samtools [04:59:30] Found java - /usr/local/bin/java [04:59:30] Found snpEff - /usr/local/bin/snpEff [04:59:30] Found samclip - /usr/local/bin/samclip [04:59:30] Found seqtk - /usr/local/bin/seqtk [04:59:30] Found parallel - /usr/local/bin/parallel [04:59:30] Found freebayes - /usr/local/bin/freebayes [04:59:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:59:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:59:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:59:30] Found vcfuniq - /usr/local/bin/vcfuniq [04:59:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:59:30] Found gzip - /bin/gzip [04:59:30] Found vt - /usr/local/bin/vt [04:59:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:59:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:59:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:59:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:59:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:59:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:59:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:59:31] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:59:45] This is snippy 4.6.0
Show full stderr[04:59:45] This is snippy 4.6.0 [04:59:45] Written by Torsten Seemann [04:59:45] Obtained from https://github.com/tseemann/snippy [04:59:45] Detected operating system: linux [04:59:45] Enabling bundled linux tools. [04:59:45] Found bwa - /usr/local/bin/bwa [04:59:45] Found bcftools - /usr/local/bin/bcftools [04:59:45] Found samtools - /usr/local/bin/samtools [04:59:45] Found java - /usr/local/bin/java [04:59:45] Found snpEff - /usr/local/bin/snpEff [04:59:45] Found samclip - /usr/local/bin/samclip [04:59:45] Found seqtk - /usr/local/bin/seqtk [04:59:45] Found parallel - /usr/local/bin/parallel [04:59:45] Found freebayes - /usr/local/bin/freebayes [04:59:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:59:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:59:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:59:45] Found vcfuniq - /usr/local/bin/vcfuniq [04:59:46] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:59:46] Found gzip - /bin/gzip [04:59:46] Found vt - /usr/local/bin/vt [04:59:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:59:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:59:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:59:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:59:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:59:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:59:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:59:46] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:01:58] This is snippy 4.6.0
Show full stderr[05:01:58] This is snippy 4.6.0 [05:01:58] Written by Torsten Seemann [05:01:58] Obtained from https://github.com/tseemann/snippy [05:01:58] Detected operating system: linux [05:01:58] Enabling bundled linux tools. [05:01:58] Found bwa - /usr/local/bin/bwa [05:01:59] Found bcftools - /usr/local/bin/bcftools [05:01:59] Found samtools - /usr/local/bin/samtools [05:01:59] Found java - /usr/local/bin/java [05:01:59] Found snpEff - /usr/local/bin/snpEff [05:01:59] Found samclip - /usr/local/bin/samclip [05:01:59] Found seqtk - /usr/local/bin/seqtk [05:01:59] Found parallel - /usr/local/bin/parallel [05:01:59] Found freebayes - /usr/local/bin/freebayes [05:01:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:01:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:01:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:01:59] Found vcfuniq - /usr/local/bin/vcfuniq [05:01:59] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:01:59] Found gzip - /bin/gzip [05:01:59] Found vt - /usr/local/bin/vt [05:01:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:01:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:01:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:01:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:01:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:02:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:02:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:02:00] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:02:02] This is snippy 4.6.0
Show full stderr[05:02:02] This is snippy 4.6.0 [05:02:02] Written by Torsten Seemann [05:02:02] Obtained from https://github.com/tseemann/snippy [05:02:02] Detected operating system: linux [05:02:02] Enabling bundled linux tools. [05:02:02] Found bwa - /usr/local/bin/bwa [05:02:02] Found bcftools - /usr/local/bin/bcftools [05:02:02] Found samtools - /usr/local/bin/samtools [05:02:02] Found java - /usr/local/bin/java [05:02:02] Found snpEff - /usr/local/bin/snpEff [05:02:02] Found samclip - /usr/local/bin/samclip [05:02:02] Found seqtk - /usr/local/bin/seqtk [05:02:02] Found parallel - /usr/local/bin/parallel [05:02:02] Found freebayes - /usr/local/bin/freebayes [05:02:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:02:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:02:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:02:02] Found vcfuniq - /usr/local/bin/vcfuniq [05:02:02] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:02:02] Found gzip - /bin/gzip [05:02:02] Found vt - /usr/local/bin/vt [05:02:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:02:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:02:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:02:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:02:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:02:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:02:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:02:03] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:02:03] This is snippy 4.6.0
Show full stderr[05:02:03] This is snippy 4.6.0 [05:02:03] Written by Torsten Seemann [05:02:03] Obtained from https://github.com/tseemann/snippy [05:02:03] Detected operating system: linux [05:02:03] Enabling bundled linux tools. [05:02:03] Found bwa - /usr/local/bin/bwa [05:02:03] Found bcftools - /usr/local/bin/bcftools [05:02:03] Found samtools - /usr/local/bin/samtools [05:02:03] Found java - /usr/local/bin/java [05:02:03] Found snpEff - /usr/local/bin/snpEff [05:02:03] Found samclip - /usr/local/bin/samclip [05:02:03] Found seqtk - /usr/local/bin/seqtk [05:02:03] Found parallel - /usr/local/bin/parallel [05:02:03] Found freebayes - /usr/local/bin/freebayes [05:02:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:02:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:02:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:02:03] Found vcfuniq - /usr/local/bin/vcfuniq [05:02:03] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:02:03] Found gzip - /bin/gzip [05:02:03] Found vt - /usr/local/bin/vt [05:02:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:02:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:02:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:02:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:02:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:02:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:02:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:02:04] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:03:10] This is snippy 4.6.0
Show full stderr[05:03:10] This is snippy 4.6.0 [05:03:10] Written by Torsten Seemann [05:03:10] Obtained from https://github.com/tseemann/snippy [05:03:10] Detected operating system: linux [05:03:10] Enabling bundled linux tools. [05:03:10] Found bwa - /usr/local/bin/bwa [05:03:10] Found bcftools - /usr/local/bin/bcftools [05:03:10] Found samtools - /usr/local/bin/samtools [05:03:10] Found java - /usr/local/bin/java [05:03:10] Found snpEff - /usr/local/bin/snpEff [05:03:10] Found samclip - /usr/local/bin/samclip [05:03:10] Found seqtk - /usr/local/bin/seqtk [05:03:10] Found parallel - /usr/local/bin/parallel [05:03:10] Found freebayes - /usr/local/bin/freebayes [05:03:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:03:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:03:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:03:10] Found vcfuniq - /usr/local/bin/vcfuniq [05:03:10] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:03:10] Found gzip - /bin/gzip [05:03:10] Found vt - /usr/local/bin/vt [05:03:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:03:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:03:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:03:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:03:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:03:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:03:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:03:11] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:03:53] This is snippy 4.6.0
Show full stderr[05:03:53] This is snippy 4.6.0 [05:03:53] Written by Torsten Seemann [05:03:53] Obtained from https://github.com/tseemann/snippy [05:03:53] Detected operating system: linux [05:03:53] Enabling bundled linux tools. [05:03:53] Found bwa - /usr/local/bin/bwa [05:03:53] Found bcftools - /usr/local/bin/bcftools [05:03:53] Found samtools - /usr/local/bin/samtools [05:03:53] Found java - /usr/local/bin/java [05:03:53] Found snpEff - /usr/local/bin/snpEff [05:03:53] Found samclip - /usr/local/bin/samclip [05:03:53] Found seqtk - /usr/local/bin/seqtk [05:03:53] Found parallel - /usr/local/bin/parallel [05:03:53] Found freebayes - /usr/local/bin/freebayes [05:03:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:03:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:03:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:03:53] Found vcfuniq - /usr/local/bin/vcfuniq [05:03:53] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:03:53] Found gzip - /bin/gzip [05:03:53] Found vt - /usr/local/bin/vt [05:03:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:03:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:03:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:03:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:03:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:03:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:03:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:03:54] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:04:59] This is snippy 4.6.0
Show full stderr[05:04:59] This is snippy 4.6.0 [05:04:59] Written by Torsten Seemann [05:04:59] Obtained from https://github.com/tseemann/snippy [05:04:59] Detected operating system: linux [05:04:59] Enabling bundled linux tools. [05:04:59] Found bwa - /usr/local/bin/bwa [05:04:59] Found bcftools - /usr/local/bin/bcftools [05:04:59] Found samtools - /usr/local/bin/samtools [05:04:59] Found java - /usr/local/bin/java [05:04:59] Found snpEff - /usr/local/bin/snpEff [05:04:59] Found samclip - /usr/local/bin/samclip [05:04:59] Found seqtk - /usr/local/bin/seqtk [05:04:59] Found parallel - /usr/local/bin/parallel [05:04:59] Found freebayes - /usr/local/bin/freebayes [05:04:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:04:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:04:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:04:59] Found vcfuniq - /usr/local/bin/vcfuniq [05:04:59] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:04:59] Found gzip - /bin/gzip [05:04:59] Found vt - /usr/local/bin/vt [05:04:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:04:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:04:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:04:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:04:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:05:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:05:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:05:00] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:59:12] This is snippy 4.6.0
Show full stderr[04:59:12] This is snippy 4.6.0 [04:59:12] Written by Torsten Seemann [04:59:12] Obtained from https://github.com/tseemann/snippy [04:59:12] Detected operating system: linux [04:59:12] Enabling bundled linux tools. [04:59:12] Found bwa - /usr/local/bin/bwa [04:59:12] Found bcftools - /usr/local/bin/bcftools [04:59:12] Found samtools - /usr/local/bin/samtools [04:59:12] Found java - /usr/local/bin/java [04:59:12] Found snpEff - /usr/local/bin/snpEff [04:59:12] Found samclip - /usr/local/bin/samclip [04:59:12] Found seqtk - /usr/local/bin/seqtk [04:59:12] Found parallel - /usr/local/bin/parallel [04:59:12] Found freebayes - /usr/local/bin/freebayes [04:59:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:59:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:59:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:59:12] Found vcfuniq - /usr/local/bin/vcfuniq [04:59:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:59:12] Found gzip - /bin/gzip [04:59:12] Found vt - /usr/local/bin/vt [04:59:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:59:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:59:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:59:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:59:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:59:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:59:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:59:13] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:59:19] This is snippy 4.6.0
Show full stderr[04:59:19] This is snippy 4.6.0 [04:59:19] Written by Torsten Seemann [04:59:19] Obtained from https://github.com/tseemann/snippy [04:59:19] Detected operating system: linux [04:59:19] Enabling bundled linux tools. [04:59:19] Found bwa - /usr/local/bin/bwa [04:59:19] Found bcftools - /usr/local/bin/bcftools [04:59:19] Found samtools - /usr/local/bin/samtools [04:59:19] Found java - /usr/local/bin/java [04:59:19] Found snpEff - /usr/local/bin/snpEff [04:59:19] Found samclip - /usr/local/bin/samclip [04:59:19] Found seqtk - /usr/local/bin/seqtk [04:59:19] Found parallel - /usr/local/bin/parallel [04:59:19] Found freebayes - /usr/local/bin/freebayes [04:59:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:59:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:59:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:59:19] Found vcfuniq - /usr/local/bin/vcfuniq [04:59:19] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:59:19] Found gzip - /bin/gzip [04:59:19] Found vt - /usr/local/bin/vt [04:59:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:59:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:59:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:59:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:59:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:59:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:59:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:59:20] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:59:51] This is snippy 4.6.0
Show full stderr[04:59:51] This is snippy 4.6.0 [04:59:51] Written by Torsten Seemann [04:59:51] Obtained from https://github.com/tseemann/snippy [04:59:51] Detected operating system: linux [04:59:51] Enabling bundled linux tools. [04:59:51] Found bwa - /usr/local/bin/bwa [04:59:51] Found bcftools - /usr/local/bin/bcftools [04:59:51] Found samtools - /usr/local/bin/samtools [04:59:51] Found java - /usr/local/bin/java [04:59:51] Found snpEff - /usr/local/bin/snpEff [04:59:51] Found samclip - /usr/local/bin/samclip [04:59:51] Found seqtk - /usr/local/bin/seqtk [04:59:51] Found parallel - /usr/local/bin/parallel [04:59:51] Found freebayes - /usr/local/bin/freebayes [04:59:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:59:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:59:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:59:51] Found vcfuniq - /usr/local/bin/vcfuniq [04:59:51] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:59:51] Found gzip - /bin/gzip [04:59:51] Found vt - /usr/local/bin/vt [04:59:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:59:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:59:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:59:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:59:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:59:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:59:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:59:52] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:00:03] This is snippy 4.6.0
Show full stderr[05:00:03] This is snippy 4.6.0 [05:00:03] Written by Torsten Seemann [05:00:03] Obtained from https://github.com/tseemann/snippy [05:00:03] Detected operating system: linux [05:00:03] Enabling bundled linux tools. [05:00:03] Found bwa - /usr/local/bin/bwa [05:00:03] Found bcftools - /usr/local/bin/bcftools [05:00:03] Found samtools - /usr/local/bin/samtools [05:00:03] Found java - /usr/local/bin/java [05:00:03] Found snpEff - /usr/local/bin/snpEff [05:00:03] Found samclip - /usr/local/bin/samclip [05:00:03] Found seqtk - /usr/local/bin/seqtk [05:00:03] Found parallel - /usr/local/bin/parallel [05:00:03] Found freebayes - /usr/local/bin/freebayes [05:00:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:00:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:00:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:00:03] Found vcfuniq - /usr/local/bin/vcfuniq [05:00:03] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:00:03] Found gzip - /bin/gzip [05:00:03] Found vt - /usr/local/bin/vt [05:00:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:00:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:00:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:00:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:00:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:00:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:00:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:00:04] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:00:34] This is snippy 4.6.0
Show full stderr[05:00:34] This is snippy 4.6.0 [05:00:34] Written by Torsten Seemann [05:00:34] Obtained from https://github.com/tseemann/snippy [05:00:34] Detected operating system: linux [05:00:34] Enabling bundled linux tools. [05:00:34] Found bwa - /usr/local/bin/bwa [05:00:34] Found bcftools - /usr/local/bin/bcftools [05:00:34] Found samtools - /usr/local/bin/samtools [05:00:34] Found java - /usr/local/bin/java [05:00:34] Found snpEff - /usr/local/bin/snpEff [05:00:34] Found samclip - /usr/local/bin/samclip [05:00:34] Found seqtk - /usr/local/bin/seqtk [05:00:34] Found parallel - /usr/local/bin/parallel [05:00:34] Found freebayes - /usr/local/bin/freebayes [05:00:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:00:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:00:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:00:34] Found vcfuniq - /usr/local/bin/vcfuniq [05:00:34] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:00:34] Found gzip - /bin/gzip [05:00:34] Found vt - /usr/local/bin/vt [05:00:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:00:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:00:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:00:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:00:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:00:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:00:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:00:35] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:00:51] This is snippy 4.6.0
Show full stderr[05:00:51] This is snippy 4.6.0 [05:00:51] Written by Torsten Seemann [05:00:51] Obtained from https://github.com/tseemann/snippy [05:00:51] Detected operating system: linux [05:00:51] Enabling bundled linux tools. [05:00:51] Found bwa - /usr/local/bin/bwa [05:00:51] Found bcftools - /usr/local/bin/bcftools [05:00:51] Found samtools - /usr/local/bin/samtools [05:00:51] Found java - /usr/local/bin/java [05:00:51] Found snpEff - /usr/local/bin/snpEff [05:00:51] Found samclip - /usr/local/bin/samclip [05:00:51] Found seqtk - /usr/local/bin/seqtk [05:00:51] Found parallel - /usr/local/bin/parallel [05:00:51] Found freebayes - /usr/local/bin/freebayes [05:00:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:00:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:00:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:00:51] Found vcfuniq - /usr/local/bin/vcfuniq [05:00:51] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:00:51] Found gzip - /bin/gzip [05:00:52] Found vt - /usr/local/bin/vt [05:00:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:00:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:00:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:00:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:00:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:00:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:00:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:00:52] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:01:12] This is snippy 4.6.0
Show full stderr[05:01:12] This is snippy 4.6.0 [05:01:12] Written by Torsten Seemann [05:01:12] Obtained from https://github.com/tseemann/snippy [05:01:12] Detected operating system: linux [05:01:12] Enabling bundled linux tools. [05:01:12] Found bwa - /usr/local/bin/bwa [05:01:12] Found bcftools - /usr/local/bin/bcftools [05:01:12] Found samtools - /usr/local/bin/samtools [05:01:12] Found java - /usr/local/bin/java [05:01:12] Found snpEff - /usr/local/bin/snpEff [05:01:12] Found samclip - /usr/local/bin/samclip [05:01:12] Found seqtk - /usr/local/bin/seqtk [05:01:12] Found parallel - /usr/local/bin/parallel [05:01:12] Found freebayes - /usr/local/bin/freebayes [05:01:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:01:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:01:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:01:12] Found vcfuniq - /usr/local/bin/vcfuniq [05:01:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:01:12] Found gzip - /bin/gzip [05:01:12] Found vt - /usr/local/bin/vt [05:01:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:01:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:01:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:01:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:01:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:01:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:01:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:01:13] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:01:40] This is snippy 4.6.0
Show full stderr[05:01:40] This is snippy 4.6.0 [05:01:40] Written by Torsten Seemann [05:01:40] Obtained from https://github.com/tseemann/snippy [05:01:40] Detected operating system: linux [05:01:40] Enabling bundled linux tools. [05:01:40] Found bwa - /usr/local/bin/bwa [05:01:40] Found bcftools - /usr/local/bin/bcftools [05:01:40] Found samtools - /usr/local/bin/samtools [05:01:40] Found java - /usr/local/bin/java [05:01:40] Found snpEff - /usr/local/bin/snpEff [05:01:40] Found samclip - /usr/local/bin/samclip [05:01:40] Found seqtk - /usr/local/bin/seqtk [05:01:40] Found parallel - /usr/local/bin/parallel [05:01:40] Found freebayes - /usr/local/bin/freebayes [05:01:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:01:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:01:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:01:40] Found vcfuniq - /usr/local/bin/vcfuniq [05:01:40] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:01:40] Found gzip - /bin/gzip [05:01:40] Found vt - /usr/local/bin/vt [05:01:41] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:01:41] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:01:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:01:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:01:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:01:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:01:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:01:41] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:02:40] This is snippy 4.6.0
Show full stderr[05:02:40] This is snippy 4.6.0 [05:02:40] Written by Torsten Seemann [05:02:40] Obtained from https://github.com/tseemann/snippy [05:02:40] Detected operating system: linux [05:02:40] Enabling bundled linux tools. [05:02:40] Found bwa - /usr/local/bin/bwa [05:02:40] Found bcftools - /usr/local/bin/bcftools [05:02:40] Found samtools - /usr/local/bin/samtools [05:02:40] Found java - /usr/local/bin/java [05:02:40] Found snpEff - /usr/local/bin/snpEff [05:02:40] Found samclip - /usr/local/bin/samclip [05:02:40] Found seqtk - /usr/local/bin/seqtk [05:02:40] Found parallel - /usr/local/bin/parallel [05:02:40] Found freebayes - /usr/local/bin/freebayes [05:02:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:02:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:02:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:02:40] Found vcfuniq - /usr/local/bin/vcfuniq [05:02:41] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:02:41] Found gzip - /bin/gzip [05:02:41] Found vt - /usr/local/bin/vt [05:02:41] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:02:41] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:02:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:02:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:02:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:02:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:02:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:02:41] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:02:41] This is snippy 4.6.0
Show full stderr[05:02:41] This is snippy 4.6.0 [05:02:41] Written by Torsten Seemann [05:02:41] Obtained from https://github.com/tseemann/snippy [05:02:41] Detected operating system: linux [05:02:41] Enabling bundled linux tools. [05:02:41] Found bwa - /usr/local/bin/bwa [05:02:41] Found bcftools - /usr/local/bin/bcftools [05:02:41] Found samtools - /usr/local/bin/samtools [05:02:41] Found java - /usr/local/bin/java [05:02:41] Found snpEff - /usr/local/bin/snpEff [05:02:41] Found samclip - /usr/local/bin/samclip [05:02:41] Found seqtk - /usr/local/bin/seqtk [05:02:41] Found parallel - /usr/local/bin/parallel [05:02:41] Found freebayes - /usr/local/bin/freebayes [05:02:41] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:02:41] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:02:41] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:02:41] Found vcfuniq - /usr/local/bin/vcfuniq [05:02:41] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:02:41] Found gzip - /bin/gzip [05:02:41] Found vt - /usr/local/bin/vt [05:02:41] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:02:41] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:02:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:02:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:02:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:02:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:02:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:02:42] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:03:20] This is snippy 4.6.0
Show full stderr[05:03:20] This is snippy 4.6.0 [05:03:20] Written by Torsten Seemann [05:03:20] Obtained from https://github.com/tseemann/snippy [05:03:20] Detected operating system: linux [05:03:20] Enabling bundled linux tools. [05:03:20] Found bwa - /usr/local/bin/bwa [05:03:20] Found bcftools - /usr/local/bin/bcftools [05:03:20] Found samtools - /usr/local/bin/samtools [05:03:20] Found java - /usr/local/bin/java [05:03:20] Found snpEff - /usr/local/bin/snpEff [05:03:20] Found samclip - /usr/local/bin/samclip [05:03:20] Found seqtk - /usr/local/bin/seqtk [05:03:20] Found parallel - /usr/local/bin/parallel [05:03:20] Found freebayes - /usr/local/bin/freebayes [05:03:20] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:03:20] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:03:20] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:03:20] Found vcfuniq - /usr/local/bin/vcfuniq [05:03:20] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:03:20] Found gzip - /bin/gzip [05:03:20] Found vt - /usr/local/bin/vt [05:03:20] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:03:20] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:03:20] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:03:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:03:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:03:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:03:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:03:21] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:03:35] This is snippy 4.6.0
Show full stderr[05:03:35] This is snippy 4.6.0 [05:03:35] Written by Torsten Seemann [05:03:35] Obtained from https://github.com/tseemann/snippy [05:03:35] Detected operating system: linux [05:03:35] Enabling bundled linux tools. [05:03:35] Found bwa - /usr/local/bin/bwa [05:03:35] Found bcftools - /usr/local/bin/bcftools [05:03:35] Found samtools - /usr/local/bin/samtools [05:03:35] Found java - /usr/local/bin/java [05:03:35] Found snpEff - /usr/local/bin/snpEff [05:03:35] Found samclip - /usr/local/bin/samclip [05:03:35] Found seqtk - /usr/local/bin/seqtk [05:03:35] Found parallel - /usr/local/bin/parallel [05:03:35] Found freebayes - /usr/local/bin/freebayes [05:03:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:03:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:03:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:03:35] Found vcfuniq - /usr/local/bin/vcfuniq [05:03:35] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:03:35] Found gzip - /bin/gzip [05:03:35] Found vt - /usr/local/bin/vt [05:03:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:03:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:03:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:03:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:03:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:03:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:03:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:03:36] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:03:38] This is snippy 4.6.0
Show full stderr[05:03:38] This is snippy 4.6.0 [05:03:38] Written by Torsten Seemann [05:03:38] Obtained from https://github.com/tseemann/snippy [05:03:38] Detected operating system: linux [05:03:38] Enabling bundled linux tools. [05:03:38] Found bwa - /usr/local/bin/bwa [05:03:38] Found bcftools - /usr/local/bin/bcftools [05:03:38] Found samtools - /usr/local/bin/samtools [05:03:38] Found java - /usr/local/bin/java [05:03:38] Found snpEff - /usr/local/bin/snpEff [05:03:38] Found samclip - /usr/local/bin/samclip [05:03:38] Found seqtk - /usr/local/bin/seqtk [05:03:38] Found parallel - /usr/local/bin/parallel [05:03:38] Found freebayes - /usr/local/bin/freebayes [05:03:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:03:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:03:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:03:38] Found vcfuniq - /usr/local/bin/vcfuniq [05:03:38] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:03:38] Found gzip - /bin/gzip [05:03:38] Found vt - /usr/local/bin/vt [05:03:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:03:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:03:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:03:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:03:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:03:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:03:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:03:39] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:04:11] This is snippy 4.6.0
Show full stderr[05:04:11] This is snippy 4.6.0 [05:04:11] Written by Torsten Seemann [05:04:11] Obtained from https://github.com/tseemann/snippy [05:04:11] Detected operating system: linux [05:04:11] Enabling bundled linux tools. [05:04:11] Found bwa - /usr/local/bin/bwa [05:04:11] Found bcftools - /usr/local/bin/bcftools [05:04:11] Found samtools - /usr/local/bin/samtools [05:04:11] Found java - /usr/local/bin/java [05:04:11] Found snpEff - /usr/local/bin/snpEff [05:04:11] Found samclip - /usr/local/bin/samclip [05:04:11] Found seqtk - /usr/local/bin/seqtk [05:04:11] Found parallel - /usr/local/bin/parallel [05:04:11] Found freebayes - /usr/local/bin/freebayes [05:04:11] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:04:11] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:04:11] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:04:11] Found vcfuniq - /usr/local/bin/vcfuniq [05:04:11] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:04:11] Found gzip - /bin/gzip [05:04:11] Found vt - /usr/local/bin/vt [05:04:11] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:04:11] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:04:11] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:04:11] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:04:11] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:04:12] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:04:12] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:04:12] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:05:30] This is snippy 4.6.0
Show full stderr[05:05:30] This is snippy 4.6.0 [05:05:30] Written by Torsten Seemann [05:05:30] Obtained from https://github.com/tseemann/snippy [05:05:30] Detected operating system: linux [05:05:30] Enabling bundled linux tools. [05:05:30] Found bwa - /usr/local/bin/bwa [05:05:30] Found bcftools - /usr/local/bin/bcftools [05:05:30] Found samtools - /usr/local/bin/samtools [05:05:30] Found java - /usr/local/bin/java [05:05:30] Found snpEff - /usr/local/bin/snpEff [05:05:30] Found samclip - /usr/local/bin/samclip [05:05:30] Found seqtk - /usr/local/bin/seqtk [05:05:30] Found parallel - /usr/local/bin/parallel [05:05:30] Found freebayes - /usr/local/bin/freebayes [05:05:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:05:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:05:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:05:30] Found vcfuniq - /usr/local/bin/vcfuniq [05:05:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:05:30] Found gzip - /bin/gzip [05:05:30] Found vt - /usr/local/bin/vt [05:05:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:05:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:05:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:05:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:05:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:05:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:05:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:05:31] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:06:03] This is snippy 4.6.0
Show full stderr[05:06:03] This is snippy 4.6.0 [05:06:03] Written by Torsten Seemann [05:06:03] Obtained from https://github.com/tseemann/snippy [05:06:03] Detected operating system: linux [05:06:03] Enabling bundled linux tools. [05:06:03] Found bwa - /usr/local/bin/bwa [05:06:03] Found bcftools - /usr/local/bin/bcftools [05:06:03] Found samtools - /usr/local/bin/samtools [05:06:03] Found java - /usr/local/bin/java [05:06:03] Found snpEff - /usr/local/bin/snpEff [05:06:03] Found samclip - /usr/local/bin/samclip [05:06:03] Found seqtk - /usr/local/bin/seqtk [05:06:03] Found parallel - /usr/local/bin/parallel [05:06:03] Found freebayes - /usr/local/bin/freebayes [05:06:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:06:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:06:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:06:03] Found vcfuniq - /usr/local/bin/vcfuniq [05:06:03] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:06:03] Found gzip - /bin/gzip [05:06:03] Found vt - /usr/local/bin/vt [05:06:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:06:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:06:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:06:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:06:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:06:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:06:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:06:04] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:07:00] This is snippy 4.6.0
Show full stderr[05:07:00] This is snippy 4.6.0 [05:07:00] Written by Torsten Seemann [05:07:00] Obtained from https://github.com/tseemann/snippy [05:07:00] Detected operating system: linux [05:07:00] Enabling bundled linux tools. [05:07:00] Found bwa - /usr/local/bin/bwa [05:07:00] Found bcftools - /usr/local/bin/bcftools [05:07:00] Found samtools - /usr/local/bin/samtools [05:07:00] Found java - /usr/local/bin/java [05:07:00] Found snpEff - /usr/local/bin/snpEff [05:07:00] Found samclip - /usr/local/bin/samclip [05:07:00] Found seqtk - /usr/local/bin/seqtk [05:07:00] Found parallel - /usr/local/bin/parallel [05:07:00] Found freebayes - /usr/local/bin/freebayes [05:07:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:07:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:07:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:07:00] Found vcfuniq - /usr/local/bin/vcfuniq [05:07:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:07:00] Found gzip - /bin/gzip [05:07:00] Found vt - /usr/local/bin/vt [05:07:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:07:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:07:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:07:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:07:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:07:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:07:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:07:01] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:00:13] This is snippy 4.6.0
Show full stderr[05:00:13] This is snippy 4.6.0 [05:00:13] Written by Torsten Seemann [05:00:13] Obtained from https://github.com/tseemann/snippy [05:00:13] Detected operating system: linux [05:00:13] Enabling bundled linux tools. [05:00:13] Found bwa - /usr/local/bin/bwa [05:00:13] Found bcftools - /usr/local/bin/bcftools [05:00:13] Found samtools - /usr/local/bin/samtools [05:00:13] Found java - /usr/local/bin/java [05:00:13] Found snpEff - /usr/local/bin/snpEff [05:00:13] Found samclip - /usr/local/bin/samclip [05:00:13] Found seqtk - /usr/local/bin/seqtk [05:00:13] Found parallel - /usr/local/bin/parallel [05:00:13] Found freebayes - /usr/local/bin/freebayes [05:00:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:00:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:00:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:00:13] Found vcfuniq - /usr/local/bin/vcfuniq [05:00:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:00:13] Found gzip - /bin/gzip [05:00:13] Found vt - /usr/local/bin/vt [05:00:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:00:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:00:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:00:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:00:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:00:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:00:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:00:14] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:00:23] This is snippy 4.6.0
Show full stderr[05:00:23] This is snippy 4.6.0 [05:00:23] Written by Torsten Seemann [05:00:23] Obtained from https://github.com/tseemann/snippy [05:00:23] Detected operating system: linux [05:00:23] Enabling bundled linux tools. [05:00:23] Found bwa - /usr/local/bin/bwa [05:00:23] Found bcftools - /usr/local/bin/bcftools [05:00:23] Found samtools - /usr/local/bin/samtools [05:00:23] Found java - /usr/local/bin/java [05:00:23] Found snpEff - /usr/local/bin/snpEff [05:00:23] Found samclip - /usr/local/bin/samclip [05:00:23] Found seqtk - /usr/local/bin/seqtk [05:00:23] Found parallel - /usr/local/bin/parallel [05:00:23] Found freebayes - /usr/local/bin/freebayes [05:00:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:00:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:00:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:00:23] Found vcfuniq - /usr/local/bin/vcfuniq [05:00:23] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:00:23] Found gzip - /bin/gzip [05:00:23] Found vt - /usr/local/bin/vt [05:00:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:00:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:00:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:00:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:00:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:00:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:00:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:00:24] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:00:39] This is snippy 4.6.0
Show full stderr[05:00:39] This is snippy 4.6.0 [05:00:39] Written by Torsten Seemann [05:00:39] Obtained from https://github.com/tseemann/snippy [05:00:39] Detected operating system: linux [05:00:39] Enabling bundled linux tools. [05:00:39] Found bwa - /usr/local/bin/bwa [05:00:39] Found bcftools - /usr/local/bin/bcftools [05:00:39] Found samtools - /usr/local/bin/samtools [05:00:39] Found java - /usr/local/bin/java [05:00:39] Found snpEff - /usr/local/bin/snpEff [05:00:39] Found samclip - /usr/local/bin/samclip [05:00:39] Found seqtk - /usr/local/bin/seqtk [05:00:39] Found parallel - /usr/local/bin/parallel [05:00:39] Found freebayes - /usr/local/bin/freebayes [05:00:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:00:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:00:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:00:39] Found vcfuniq - /usr/local/bin/vcfuniq [05:00:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:00:39] Found gzip - /bin/gzip [05:00:39] Found vt - /usr/local/bin/vt [05:00:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:00:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:00:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:00:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:00:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:00:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:00:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:00:40] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:00:48] This is snippy 4.6.0
Show full stderr[05:00:48] This is snippy 4.6.0 [05:00:48] Written by Torsten Seemann [05:00:48] Obtained from https://github.com/tseemann/snippy [05:00:48] Detected operating system: linux [05:00:48] Enabling bundled linux tools. [05:00:48] Found bwa - /usr/local/bin/bwa [05:00:48] Found bcftools - /usr/local/bin/bcftools [05:00:49] Found samtools - /usr/local/bin/samtools [05:00:49] Found java - /usr/local/bin/java [05:00:49] Found snpEff - /usr/local/bin/snpEff [05:00:49] Found samclip - /usr/local/bin/samclip [05:00:49] Found seqtk - /usr/local/bin/seqtk [05:00:49] Found parallel - /usr/local/bin/parallel [05:00:49] Found freebayes - /usr/local/bin/freebayes [05:00:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:00:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:00:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:00:49] Found vcfuniq - /usr/local/bin/vcfuniq [05:00:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:00:49] Found gzip - /bin/gzip [05:00:49] Found vt - /usr/local/bin/vt [05:00:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:00:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:00:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:00:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:00:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:00:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:00:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:00:49] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:00:55] This is snippy 4.6.0
Show full stderr[05:00:55] This is snippy 4.6.0 [05:00:55] Written by Torsten Seemann [05:00:55] Obtained from https://github.com/tseemann/snippy [05:00:55] Detected operating system: linux [05:00:55] Enabling bundled linux tools. [05:00:55] Found bwa - /usr/local/bin/bwa [05:00:55] Found bcftools - /usr/local/bin/bcftools [05:00:55] Found samtools - /usr/local/bin/samtools [05:00:55] Found java - /usr/local/bin/java [05:00:55] Found snpEff - /usr/local/bin/snpEff [05:00:55] Found samclip - /usr/local/bin/samclip [05:00:55] Found seqtk - /usr/local/bin/seqtk [05:00:55] Found parallel - /usr/local/bin/parallel [05:00:55] Found freebayes - /usr/local/bin/freebayes [05:00:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:00:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:00:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:00:55] Found vcfuniq - /usr/local/bin/vcfuniq [05:00:55] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:00:55] Found gzip - /bin/gzip [05:00:55] Found vt - /usr/local/bin/vt [05:00:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:00:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:00:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:00:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:00:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:00:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:00:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:00:56] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:01:22] This is snippy 4.6.0
Show full stderr[05:01:22] This is snippy 4.6.0 [05:01:22] Written by Torsten Seemann [05:01:22] Obtained from https://github.com/tseemann/snippy [05:01:22] Detected operating system: linux [05:01:22] Enabling bundled linux tools. [05:01:22] Found bwa - /usr/local/bin/bwa [05:01:22] Found bcftools - /usr/local/bin/bcftools [05:01:22] Found samtools - /usr/local/bin/samtools [05:01:22] Found java - /usr/local/bin/java [05:01:22] Found snpEff - /usr/local/bin/snpEff [05:01:22] Found samclip - /usr/local/bin/samclip [05:01:22] Found seqtk - /usr/local/bin/seqtk [05:01:22] Found parallel - /usr/local/bin/parallel [05:01:22] Found freebayes - /usr/local/bin/freebayes [05:01:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:01:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:01:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:01:22] Found vcfuniq - /usr/local/bin/vcfuniq [05:01:22] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:01:22] Found gzip - /bin/gzip [05:01:22] Found vt - /usr/local/bin/vt [05:01:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:01:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:01:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:01:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:01:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:01:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:01:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:01:23] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:01:34] This is snippy 4.6.0
Show full stderr[05:01:34] This is snippy 4.6.0 [05:01:34] Written by Torsten Seemann [05:01:34] Obtained from https://github.com/tseemann/snippy [05:01:34] Detected operating system: linux [05:01:34] Enabling bundled linux tools. [05:01:34] Found bwa - /usr/local/bin/bwa [05:01:34] Found bcftools - /usr/local/bin/bcftools [05:01:34] Found samtools - /usr/local/bin/samtools [05:01:34] Found java - /usr/local/bin/java [05:01:34] Found snpEff - /usr/local/bin/snpEff [05:01:34] Found samclip - /usr/local/bin/samclip [05:01:34] Found seqtk - /usr/local/bin/seqtk [05:01:34] Found parallel - /usr/local/bin/parallel [05:01:34] Found freebayes - /usr/local/bin/freebayes [05:01:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:01:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:01:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:01:34] Found vcfuniq - /usr/local/bin/vcfuniq [05:01:34] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:01:34] Found gzip - /bin/gzip [05:01:34] Found vt - /usr/local/bin/vt [05:01:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:01:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:01:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:01:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:01:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:01:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:01:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:01:35] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:01:47] This is snippy 4.6.0
Show full stderr[05:01:47] This is snippy 4.6.0 [05:01:47] Written by Torsten Seemann [05:01:47] Obtained from https://github.com/tseemann/snippy [05:01:47] Detected operating system: linux [05:01:47] Enabling bundled linux tools. [05:01:47] Found bwa - /usr/local/bin/bwa [05:01:47] Found bcftools - /usr/local/bin/bcftools [05:01:47] Found samtools - /usr/local/bin/samtools [05:01:47] Found java - /usr/local/bin/java [05:01:47] Found snpEff - /usr/local/bin/snpEff [05:01:47] Found samclip - /usr/local/bin/samclip [05:01:47] Found seqtk - /usr/local/bin/seqtk [05:01:47] Found parallel - /usr/local/bin/parallel [05:01:47] Found freebayes - /usr/local/bin/freebayes [05:01:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:01:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:01:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:01:47] Found vcfuniq - /usr/local/bin/vcfuniq [05:01:47] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:01:47] Found gzip - /bin/gzip [05:01:47] Found vt - /usr/local/bin/vt [05:01:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:01:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:01:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:01:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:01:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:01:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:01:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:01:48] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:02:24] This is snippy 4.6.0
Show full stderr[05:02:24] This is snippy 4.6.0 [05:02:24] Written by Torsten Seemann [05:02:24] Obtained from https://github.com/tseemann/snippy [05:02:24] Detected operating system: linux [05:02:24] Enabling bundled linux tools. [05:02:24] Found bwa - /usr/local/bin/bwa [05:02:24] Found bcftools - /usr/local/bin/bcftools [05:02:24] Found samtools - /usr/local/bin/samtools [05:02:24] Found java - /usr/local/bin/java [05:02:24] Found snpEff - /usr/local/bin/snpEff [05:02:24] Found samclip - /usr/local/bin/samclip [05:02:24] Found seqtk - /usr/local/bin/seqtk [05:02:24] Found parallel - /usr/local/bin/parallel [05:02:24] Found freebayes - /usr/local/bin/freebayes [05:02:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:02:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:02:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:02:24] Found vcfuniq - /usr/local/bin/vcfuniq [05:02:24] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:02:24] Found gzip - /bin/gzip [05:02:24] Found vt - /usr/local/bin/vt [05:02:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:02:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:02:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:02:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:02:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:02:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:02:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:02:25] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:02:35] This is snippy 4.6.0
Show full stderr[05:02:35] This is snippy 4.6.0 [05:02:35] Written by Torsten Seemann [05:02:35] Obtained from https://github.com/tseemann/snippy [05:02:35] Detected operating system: linux [05:02:35] Enabling bundled linux tools. [05:02:35] Found bwa - /usr/local/bin/bwa [05:02:35] Found bcftools - /usr/local/bin/bcftools [05:02:35] Found samtools - /usr/local/bin/samtools [05:02:35] Found java - /usr/local/bin/java [05:02:35] Found snpEff - /usr/local/bin/snpEff [05:02:35] Found samclip - /usr/local/bin/samclip [05:02:35] Found seqtk - /usr/local/bin/seqtk [05:02:35] Found parallel - /usr/local/bin/parallel [05:02:35] Found freebayes - /usr/local/bin/freebayes [05:02:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:02:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:02:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:02:35] Found vcfuniq - /usr/local/bin/vcfuniq [05:02:35] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:02:35] Found gzip - /bin/gzip [05:02:35] Found vt - /usr/local/bin/vt [05:02:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:02:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:02:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:02:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:02:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:02:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:02:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:02:35] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:02:26] This is snippy 4.6.0
Show full stderr[05:02:26] This is snippy 4.6.0 [05:02:26] Written by Torsten Seemann [05:02:26] Obtained from https://github.com/tseemann/snippy [05:02:26] Detected operating system: linux [05:02:26] Enabling bundled linux tools. [05:02:26] Found bwa - /usr/local/bin/bwa [05:02:26] Found bcftools - /usr/local/bin/bcftools [05:02:26] Found samtools - /usr/local/bin/samtools [05:02:26] Found java - /usr/local/bin/java [05:02:26] Found snpEff - /usr/local/bin/snpEff [05:02:27] Found samclip - /usr/local/bin/samclip [05:02:27] Found seqtk - /usr/local/bin/seqtk [05:02:27] Found parallel - /usr/local/bin/parallel [05:02:27] Found freebayes - /usr/local/bin/freebayes [05:02:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:02:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:02:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:02:27] Found vcfuniq - /usr/local/bin/vcfuniq [05:02:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:02:27] Found gzip - /bin/gzip [05:02:27] Found vt - /usr/local/bin/vt [05:02:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:02:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:02:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:02:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:02:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:02:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:02:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:02:27] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:02:58] This is snippy 4.6.0
Show full stderr[05:02:58] This is snippy 4.6.0 [05:02:58] Written by Torsten Seemann [05:02:58] Obtained from https://github.com/tseemann/snippy [05:02:58] Detected operating system: linux [05:02:58] Enabling bundled linux tools. [05:02:58] Found bwa - /usr/local/bin/bwa [05:02:58] Found bcftools - /usr/local/bin/bcftools [05:02:58] Found samtools - /usr/local/bin/samtools [05:02:58] Found java - /usr/local/bin/java [05:02:58] Found snpEff - /usr/local/bin/snpEff [05:02:58] Found samclip - /usr/local/bin/samclip [05:02:58] Found seqtk - /usr/local/bin/seqtk [05:02:58] Found parallel - /usr/local/bin/parallel [05:02:58] Found freebayes - /usr/local/bin/freebayes [05:02:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:02:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:02:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:02:58] Found vcfuniq - /usr/local/bin/vcfuniq [05:02:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:02:58] Found gzip - /bin/gzip [05:02:58] Found vt - /usr/local/bin/vt [05:02:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:02:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:02:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:02:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:02:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:02:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:02:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:02:59] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:03:23] This is snippy 4.6.0
Show full stderr[05:03:23] This is snippy 4.6.0 [05:03:23] Written by Torsten Seemann [05:03:23] Obtained from https://github.com/tseemann/snippy [05:03:23] Detected operating system: linux [05:03:23] Enabling bundled linux tools. [05:03:23] Found bwa - /usr/local/bin/bwa [05:03:23] Found bcftools - /usr/local/bin/bcftools [05:03:23] Found samtools - /usr/local/bin/samtools [05:03:23] Found java - /usr/local/bin/java [05:03:23] Found snpEff - /usr/local/bin/snpEff [05:03:23] Found samclip - /usr/local/bin/samclip [05:03:23] Found seqtk - /usr/local/bin/seqtk [05:03:23] Found parallel - /usr/local/bin/parallel [05:03:23] Found freebayes - /usr/local/bin/freebayes [05:03:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:03:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:03:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:03:23] Found vcfuniq - /usr/local/bin/vcfuniq [05:03:23] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:03:23] Found gzip - /bin/gzip [05:03:23] Found vt - /usr/local/bin/vt [05:03:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:03:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:03:23] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:03:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:03:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:03:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:03:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:03:24] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:03:26] This is snippy 4.6.0
Show full stderr[05:03:26] This is snippy 4.6.0 [05:03:26] Written by Torsten Seemann [05:03:26] Obtained from https://github.com/tseemann/snippy [05:03:26] Detected operating system: linux [05:03:26] Enabling bundled linux tools. [05:03:26] Found bwa - /usr/local/bin/bwa [05:03:26] Found bcftools - /usr/local/bin/bcftools [05:03:26] Found samtools - /usr/local/bin/samtools [05:03:26] Found java - /usr/local/bin/java [05:03:26] Found snpEff - /usr/local/bin/snpEff [05:03:26] Found samclip - /usr/local/bin/samclip [05:03:26] Found seqtk - /usr/local/bin/seqtk [05:03:26] Found parallel - /usr/local/bin/parallel [05:03:26] Found freebayes - /usr/local/bin/freebayes [05:03:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:03:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:03:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:03:26] Found vcfuniq - /usr/local/bin/vcfuniq [05:03:26] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:03:26] Found gzip - /bin/gzip [05:03:26] Found vt - /usr/local/bin/vt [05:03:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:03:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:03:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:03:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:03:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:03:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:03:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:03:27] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:03:43] This is snippy 4.6.0
Show full stderr[05:03:43] This is snippy 4.6.0 [05:03:43] Written by Torsten Seemann [05:03:43] Obtained from https://github.com/tseemann/snippy [05:03:43] Detected operating system: linux [05:03:43] Enabling bundled linux tools. [05:03:43] Found bwa - /usr/local/bin/bwa [05:03:43] Found bcftools - /usr/local/bin/bcftools [05:03:43] Found samtools - /usr/local/bin/samtools [05:03:43] Found java - /usr/local/bin/java [05:03:43] Found snpEff - /usr/local/bin/snpEff [05:03:43] Found samclip - /usr/local/bin/samclip [05:03:43] Found seqtk - /usr/local/bin/seqtk [05:03:43] Found parallel - /usr/local/bin/parallel [05:03:43] Found freebayes - /usr/local/bin/freebayes [05:03:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:03:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:03:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:03:43] Found vcfuniq - /usr/local/bin/vcfuniq [05:03:43] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:03:43] Found gzip - /bin/gzip [05:03:43] Found vt - /usr/local/bin/vt [05:03:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:03:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:03:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:03:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:03:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:03:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:03:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:03:44] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:04:43] This is snippy 4.6.0
Show full stderr[05:04:43] This is snippy 4.6.0 [05:04:43] Written by Torsten Seemann [05:04:43] Obtained from https://github.com/tseemann/snippy [05:04:43] Detected operating system: linux [05:04:43] Enabling bundled linux tools. [05:04:43] Found bwa - /usr/local/bin/bwa [05:04:43] Found bcftools - /usr/local/bin/bcftools [05:04:43] Found samtools - /usr/local/bin/samtools [05:04:43] Found java - /usr/local/bin/java [05:04:43] Found snpEff - /usr/local/bin/snpEff [05:04:43] Found samclip - /usr/local/bin/samclip [05:04:43] Found seqtk - /usr/local/bin/seqtk [05:04:43] Found parallel - /usr/local/bin/parallel [05:04:43] Found freebayes - /usr/local/bin/freebayes [05:04:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:04:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:04:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:04:43] Found vcfuniq - /usr/local/bin/vcfuniq [05:04:43] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:04:43] Found gzip - /bin/gzip [05:04:43] Found vt - /usr/local/bin/vt [05:04:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:04:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:04:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:04:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:04:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:04:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:04:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:04:44] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:04:41] This is snippy 4.6.0
Show full stderr[05:04:41] This is snippy 4.6.0 [05:04:41] Written by Torsten Seemann [05:04:41] Obtained from https://github.com/tseemann/snippy [05:04:41] Detected operating system: linux [05:04:41] Enabling bundled linux tools. [05:04:41] Found bwa - /usr/local/bin/bwa [05:04:41] Found bcftools - /usr/local/bin/bcftools [05:04:41] Found samtools - /usr/local/bin/samtools [05:04:41] Found java - /usr/local/bin/java [05:04:41] Found snpEff - /usr/local/bin/snpEff [05:04:41] Found samclip - /usr/local/bin/samclip [05:04:41] Found seqtk - /usr/local/bin/seqtk [05:04:41] Found parallel - /usr/local/bin/parallel [05:04:41] Found freebayes - /usr/local/bin/freebayes [05:04:41] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:04:41] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:04:41] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:04:41] Found vcfuniq - /usr/local/bin/vcfuniq [05:04:41] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:04:41] Found gzip - /bin/gzip [05:04:41] Found vt - /usr/local/bin/vt [05:04:41] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:04:41] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:04:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:04:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:04:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:04:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:04:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:04:42] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:05:57] This is snippy 4.6.0
Show full stderr[05:05:57] This is snippy 4.6.0 [05:05:57] Written by Torsten Seemann [05:05:57] Obtained from https://github.com/tseemann/snippy [05:05:57] Detected operating system: linux [05:05:57] Enabling bundled linux tools. [05:05:57] Found bwa - /usr/local/bin/bwa [05:05:57] Found bcftools - /usr/local/bin/bcftools [05:05:57] Found samtools - /usr/local/bin/samtools [05:05:57] Found java - /usr/local/bin/java [05:05:57] Found snpEff - /usr/local/bin/snpEff [05:05:57] Found samclip - /usr/local/bin/samclip [05:05:57] Found seqtk - /usr/local/bin/seqtk [05:05:57] Found parallel - /usr/local/bin/parallel [05:05:57] Found freebayes - /usr/local/bin/freebayes [05:05:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:05:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:05:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:05:57] Found vcfuniq - /usr/local/bin/vcfuniq [05:05:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:05:57] Found gzip - /bin/gzip [05:05:57] Found vt - /usr/local/bin/vt [05:05:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:05:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:05:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:05:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:05:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:05:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:05:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:05:58] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:06:02] This is snippy 4.6.0
Show full stderr[05:06:02] This is snippy 4.6.0 [05:06:02] Written by Torsten Seemann [05:06:02] Obtained from https://github.com/tseemann/snippy [05:06:02] Detected operating system: linux [05:06:02] Enabling bundled linux tools. [05:06:02] Found bwa - /usr/local/bin/bwa [05:06:02] Found bcftools - /usr/local/bin/bcftools [05:06:02] Found samtools - /usr/local/bin/samtools [05:06:02] Found java - /usr/local/bin/java [05:06:02] Found snpEff - /usr/local/bin/snpEff [05:06:02] Found samclip - /usr/local/bin/samclip [05:06:02] Found seqtk - /usr/local/bin/seqtk [05:06:02] Found parallel - /usr/local/bin/parallel [05:06:02] Found freebayes - /usr/local/bin/freebayes [05:06:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:06:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:06:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:06:02] Found vcfuniq - /usr/local/bin/vcfuniq [05:06:02] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:06:02] Found gzip - /bin/gzip [05:06:02] Found vt - /usr/local/bin/vt [05:06:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:06:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:06:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:06:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:06:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:06:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:06:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:06:03] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:07:42] This is snippy 4.6.0
Show full stderr[05:07:42] This is snippy 4.6.0 [05:07:42] Written by Torsten Seemann [05:07:42] Obtained from https://github.com/tseemann/snippy [05:07:42] Detected operating system: linux [05:07:42] Enabling bundled linux tools. [05:07:42] Found bwa - /usr/local/bin/bwa [05:07:42] Found bcftools - /usr/local/bin/bcftools [05:07:42] Found samtools - /usr/local/bin/samtools [05:07:42] Found java - /usr/local/bin/java [05:07:42] Found snpEff - /usr/local/bin/snpEff [05:07:42] Found samclip - /usr/local/bin/samclip [05:07:42] Found seqtk - /usr/local/bin/seqtk [05:07:42] Found parallel - /usr/local/bin/parallel [05:07:42] Found freebayes - /usr/local/bin/freebayes [05:07:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:07:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:07:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:07:42] Found vcfuniq - /usr/local/bin/vcfuniq [05:07:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:07:42] Found gzip - /bin/gzip [05:07:42] Found vt - /usr/local/bin/vt [05:07:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:07:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:07:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:07:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:07:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:07:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:07:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:07:43] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:08:27] This is snippy 4.6.0
Show full stderr[05:08:27] This is snippy 4.6.0 [05:08:27] Written by Torsten Seemann [05:08:27] Obtained from https://github.com/tseemann/snippy [05:08:27] Detected operating system: linux [05:08:27] Enabling bundled linux tools. [05:08:27] Found bwa - /usr/local/bin/bwa [05:08:27] Found bcftools - /usr/local/bin/bcftools [05:08:27] Found samtools - /usr/local/bin/samtools [05:08:27] Found java - /usr/local/bin/java [05:08:27] Found snpEff - /usr/local/bin/snpEff [05:08:27] Found samclip - /usr/local/bin/samclip [05:08:27] Found seqtk - /usr/local/bin/seqtk [05:08:27] Found parallel - /usr/local/bin/parallel [05:08:27] Found freebayes - /usr/local/bin/freebayes [05:08:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:08:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:08:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:08:27] Found vcfuniq - /usr/local/bin/vcfuniq [05:08:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:08:27] Found gzip - /bin/gzip [05:08:27] Found vt - /usr/local/bin/vt [05:08:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:08:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:08:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:08:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:08:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:08:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:08:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:08:28] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:07:43] This is snippy 4.6.0
Show full stderr[05:07:43] This is snippy 4.6.0 [05:07:43] Written by Torsten Seemann [05:07:43] Obtained from https://github.com/tseemann/snippy [05:07:43] Detected operating system: linux [05:07:43] Enabling bundled linux tools. [05:07:43] Found bwa - /usr/local/bin/bwa [05:07:43] Found bcftools - /usr/local/bin/bcftools [05:07:43] Found samtools - /usr/local/bin/samtools [05:07:43] Found java - /usr/local/bin/java [05:07:43] Found snpEff - /usr/local/bin/snpEff [05:07:43] Found samclip - /usr/local/bin/samclip [05:07:43] Found seqtk - /usr/local/bin/seqtk [05:07:43] Found parallel - /usr/local/bin/parallel [05:07:43] Found freebayes - /usr/local/bin/freebayes [05:07:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:07:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:07:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:07:43] Found vcfuniq - /usr/local/bin/vcfuniq [05:07:43] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:07:43] Found gzip - /bin/gzip [05:07:43] Found vt - /usr/local/bin/vt [05:07:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:07:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:07:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:07:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:07:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:07:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:07:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:07:44] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:07:48] This is snippy 4.6.0
Show full stderr[05:07:48] This is snippy 4.6.0 [05:07:48] Written by Torsten Seemann [05:07:48] Obtained from https://github.com/tseemann/snippy [05:07:48] Detected operating system: linux [05:07:48] Enabling bundled linux tools. [05:07:48] Found bwa - /usr/local/bin/bwa [05:07:48] Found bcftools - /usr/local/bin/bcftools [05:07:48] Found samtools - /usr/local/bin/samtools [05:07:48] Found java - /usr/local/bin/java [05:07:48] Found snpEff - /usr/local/bin/snpEff [05:07:48] Found samclip - /usr/local/bin/samclip [05:07:48] Found seqtk - /usr/local/bin/seqtk [05:07:48] Found parallel - /usr/local/bin/parallel [05:07:48] Found freebayes - /usr/local/bin/freebayes [05:07:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:07:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:07:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:07:48] Found vcfuniq - /usr/local/bin/vcfuniq [05:07:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:07:48] Found gzip - /bin/gzip [05:07:48] Found vt - /usr/local/bin/vt [05:07:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:07:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:07:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:07:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:07:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:07:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:07:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:07:49] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:07:54] This is snippy 4.6.0
Show full stderr[05:07:54] This is snippy 4.6.0 [05:07:54] Written by Torsten Seemann [05:07:54] Obtained from https://github.com/tseemann/snippy [05:07:54] Detected operating system: linux [05:07:54] Enabling bundled linux tools. [05:07:54] Found bwa - /usr/local/bin/bwa [05:07:54] Found bcftools - /usr/local/bin/bcftools [05:07:54] Found samtools - /usr/local/bin/samtools [05:07:54] Found java - /usr/local/bin/java [05:07:54] Found snpEff - /usr/local/bin/snpEff [05:07:54] Found samclip - /usr/local/bin/samclip [05:07:54] Found seqtk - /usr/local/bin/seqtk [05:07:54] Found parallel - /usr/local/bin/parallel [05:07:54] Found freebayes - /usr/local/bin/freebayes [05:07:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:07:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:07:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:07:54] Found vcfuniq - /usr/local/bin/vcfuniq [05:07:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:07:54] Found gzip - /bin/gzip [05:07:54] Found vt - /usr/local/bin/vt [05:07:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:07:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:07:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:07:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:07:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:07:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:07:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:07:55] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:08:03] This is snippy 4.6.0
Show full stderr[05:08:03] This is snippy 4.6.0 [05:08:03] Written by Torsten Seemann [05:08:03] Obtained from https://github.com/tseemann/snippy [05:08:03] Detected operating system: linux [05:08:03] Enabling bundled linux tools. [05:08:03] Found bwa - /usr/local/bin/bwa [05:08:03] Found bcftools - /usr/local/bin/bcftools [05:08:03] Found samtools - /usr/local/bin/samtools [05:08:03] Found java - /usr/local/bin/java [05:08:03] Found snpEff - /usr/local/bin/snpEff [05:08:03] Found samclip - /usr/local/bin/samclip [05:08:03] Found seqtk - /usr/local/bin/seqtk [05:08:03] Found parallel - /usr/local/bin/parallel [05:08:03] Found freebayes - /usr/local/bin/freebayes [05:08:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:08:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:08:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:08:03] Found vcfuniq - /usr/local/bin/vcfuniq [05:08:03] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:08:03] Found gzip - /bin/gzip [05:08:03] Found vt - /usr/local/bin/vt [05:08:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:08:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:08:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:08:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:08:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:08:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:08:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:08:04] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:08:54] This is snippy 4.6.0
Show full stderr[05:08:54] This is snippy 4.6.0 [05:08:54] Written by Torsten Seemann [05:08:54] Obtained from https://github.com/tseemann/snippy [05:08:54] Detected operating system: linux [05:08:54] Enabling bundled linux tools. [05:08:54] Found bwa - /usr/local/bin/bwa [05:08:54] Found bcftools - /usr/local/bin/bcftools [05:08:54] Found samtools - /usr/local/bin/samtools [05:08:54] Found java - /usr/local/bin/java [05:08:54] Found snpEff - /usr/local/bin/snpEff [05:08:54] Found samclip - /usr/local/bin/samclip [05:08:54] Found seqtk - /usr/local/bin/seqtk [05:08:54] Found parallel - /usr/local/bin/parallel [05:08:54] Found freebayes - /usr/local/bin/freebayes [05:08:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:08:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:08:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:08:54] Found vcfuniq - /usr/local/bin/vcfuniq [05:08:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:08:54] Found gzip - /bin/gzip [05:08:54] Found vt - /usr/local/bin/vt [05:08:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:08:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:08:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:08:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:08:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:08:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:08:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:08:55] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:02:54] This is snippy 4.6.0
Show full stderr[05:02:54] This is snippy 4.6.0 [05:02:54] Written by Torsten Seemann [05:02:54] Obtained from https://github.com/tseemann/snippy [05:02:54] Detected operating system: linux [05:02:54] Enabling bundled linux tools. [05:02:54] Found bwa - /usr/local/bin/bwa [05:02:54] Found bcftools - /usr/local/bin/bcftools [05:02:54] Found samtools - /usr/local/bin/samtools [05:02:54] Found java - /usr/local/bin/java [05:02:55] Found snpEff - /usr/local/bin/snpEff [05:02:55] Found samclip - /usr/local/bin/samclip [05:02:55] Found seqtk - /usr/local/bin/seqtk [05:02:55] Found parallel - /usr/local/bin/parallel [05:02:55] Found freebayes - /usr/local/bin/freebayes [05:02:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:02:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:02:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:02:55] Found vcfuniq - /usr/local/bin/vcfuniq [05:02:55] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:02:55] Found gzip - /bin/gzip [05:02:55] Found vt - /usr/local/bin/vt [05:02:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:02:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:02:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:02:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:02:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:02:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:02:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:02:55] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:03:17] This is snippy 4.6.0
Show full stderr[05:03:17] This is snippy 4.6.0 [05:03:17] Written by Torsten Seemann [05:03:17] Obtained from https://github.com/tseemann/snippy [05:03:17] Detected operating system: linux [05:03:17] Enabling bundled linux tools. [05:03:17] Found bwa - /usr/local/bin/bwa [05:03:17] Found bcftools - /usr/local/bin/bcftools [05:03:17] Found samtools - /usr/local/bin/samtools [05:03:17] Found java - /usr/local/bin/java [05:03:17] Found snpEff - /usr/local/bin/snpEff [05:03:17] Found samclip - /usr/local/bin/samclip [05:03:17] Found seqtk - /usr/local/bin/seqtk [05:03:17] Found parallel - /usr/local/bin/parallel [05:03:17] Found freebayes - /usr/local/bin/freebayes [05:03:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:03:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:03:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:03:17] Found vcfuniq - /usr/local/bin/vcfuniq [05:03:17] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:03:17] Found gzip - /bin/gzip [05:03:17] Found vt - /usr/local/bin/vt [05:03:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:03:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:03:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:03:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:03:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:03:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:03:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:03:18] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:03:50] This is snippy 4.6.0
Show full stderr[05:03:50] This is snippy 4.6.0 [05:03:50] Written by Torsten Seemann [05:03:50] Obtained from https://github.com/tseemann/snippy [05:03:50] Detected operating system: linux [05:03:50] Enabling bundled linux tools. [05:03:50] Found bwa - /usr/local/bin/bwa [05:03:50] Found bcftools - /usr/local/bin/bcftools [05:03:50] Found samtools - /usr/local/bin/samtools [05:03:50] Found java - /usr/local/bin/java [05:03:50] Found snpEff - /usr/local/bin/snpEff [05:03:50] Found samclip - /usr/local/bin/samclip [05:03:50] Found seqtk - /usr/local/bin/seqtk [05:03:50] Found parallel - /usr/local/bin/parallel [05:03:50] Found freebayes - /usr/local/bin/freebayes [05:03:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:03:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:03:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:03:50] Found vcfuniq - /usr/local/bin/vcfuniq [05:03:50] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:03:50] Found gzip - /bin/gzip [05:03:50] Found vt - /usr/local/bin/vt [05:03:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:03:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:03:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:03:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:03:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:03:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:03:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:03:51] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:04:10] This is snippy 4.6.0
Show full stderr[05:04:10] This is snippy 4.6.0 [05:04:10] Written by Torsten Seemann [05:04:10] Obtained from https://github.com/tseemann/snippy [05:04:10] Detected operating system: linux [05:04:10] Enabling bundled linux tools. [05:04:10] Found bwa - /usr/local/bin/bwa [05:04:10] Found bcftools - /usr/local/bin/bcftools [05:04:10] Found samtools - /usr/local/bin/samtools [05:04:10] Found java - /usr/local/bin/java [05:04:10] Found snpEff - /usr/local/bin/snpEff [05:04:10] Found samclip - /usr/local/bin/samclip [05:04:10] Found seqtk - /usr/local/bin/seqtk [05:04:10] Found parallel - /usr/local/bin/parallel [05:04:10] Found freebayes - /usr/local/bin/freebayes [05:04:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:04:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:04:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:04:10] Found vcfuniq - /usr/local/bin/vcfuniq [05:04:10] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:04:10] Found gzip - /bin/gzip [05:04:10] Found vt - /usr/local/bin/vt [05:04:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:04:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:04:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:04:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:04:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:04:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:04:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:04:10] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:09:49] This is snippy 4.6.0
Show full stderr[05:09:49] This is snippy 4.6.0 [05:09:49] Written by Torsten Seemann [05:09:49] Obtained from https://github.com/tseemann/snippy [05:09:49] Detected operating system: linux [05:09:49] Enabling bundled linux tools. [05:09:49] Found bwa - /usr/local/bin/bwa [05:09:49] Found bcftools - /usr/local/bin/bcftools [05:09:49] Found samtools - /usr/local/bin/samtools [05:09:49] Found java - /usr/local/bin/java [05:09:49] Found snpEff - /usr/local/bin/snpEff [05:09:49] Found samclip - /usr/local/bin/samclip [05:09:49] Found seqtk - /usr/local/bin/seqtk [05:09:49] Found parallel - /usr/local/bin/parallel [05:09:49] Found freebayes - /usr/local/bin/freebayes [05:09:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:09:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:09:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:09:49] Found vcfuniq - /usr/local/bin/vcfuniq [05:09:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:09:49] Found gzip - /bin/gzip [05:09:49] Found vt - /usr/local/bin/vt [05:09:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:09:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:09:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:09:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:09:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:09:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:09:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:09:53] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:10:03] This is snippy 4.6.0
Show full stderr[05:10:03] This is snippy 4.6.0 [05:10:03] Written by Torsten Seemann [05:10:03] Obtained from https://github.com/tseemann/snippy [05:10:03] Detected operating system: linux [05:10:03] Enabling bundled linux tools. [05:10:03] Found bwa - /usr/local/bin/bwa [05:10:03] Found bcftools - /usr/local/bin/bcftools [05:10:03] Found samtools - /usr/local/bin/samtools [05:10:03] Found java - /usr/local/bin/java [05:10:03] Found snpEff - /usr/local/bin/snpEff [05:10:03] Found samclip - /usr/local/bin/samclip [05:10:03] Found seqtk - /usr/local/bin/seqtk [05:10:03] Found parallel - /usr/local/bin/parallel [05:10:03] Found freebayes - /usr/local/bin/freebayes [05:10:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:10:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:10:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:10:03] Found vcfuniq - /usr/local/bin/vcfuniq [05:10:03] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:10:03] Found gzip - /bin/gzip [05:10:03] Found vt - /usr/local/bin/vt [05:10:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:10:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:10:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:10:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:10:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:10:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:10:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:10:04] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:10:40] This is snippy 4.6.0
Show full stderr[05:10:40] This is snippy 4.6.0 [05:10:40] Written by Torsten Seemann [05:10:40] Obtained from https://github.com/tseemann/snippy [05:10:40] Detected operating system: linux [05:10:40] Enabling bundled linux tools. [05:10:40] Found bwa - /usr/local/bin/bwa [05:10:40] Found bcftools - /usr/local/bin/bcftools [05:10:40] Found samtools - /usr/local/bin/samtools [05:10:40] Found java - /usr/local/bin/java [05:10:40] Found snpEff - /usr/local/bin/snpEff [05:10:40] Found samclip - /usr/local/bin/samclip [05:10:40] Found seqtk - /usr/local/bin/seqtk [05:10:40] Found parallel - /usr/local/bin/parallel [05:10:40] Found freebayes - /usr/local/bin/freebayes [05:10:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:10:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:10:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:10:40] Found vcfuniq - /usr/local/bin/vcfuniq [05:10:40] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:10:40] Found gzip - /bin/gzip [05:10:40] Found vt - /usr/local/bin/vt [05:10:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:10:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:10:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:10:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:10:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:10:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:10:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:10:40] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:10:49] This is snippy 4.6.0
Show full stderr[05:10:49] This is snippy 4.6.0 [05:10:49] Written by Torsten Seemann [05:10:49] Obtained from https://github.com/tseemann/snippy [05:10:49] Detected operating system: linux [05:10:49] Enabling bundled linux tools. [05:10:49] Found bwa - /usr/local/bin/bwa [05:10:49] Found bcftools - /usr/local/bin/bcftools [05:10:49] Found samtools - /usr/local/bin/samtools [05:10:49] Found java - /usr/local/bin/java [05:10:49] Found snpEff - /usr/local/bin/snpEff [05:10:49] Found samclip - /usr/local/bin/samclip [05:10:49] Found seqtk - /usr/local/bin/seqtk [05:10:49] Found parallel - /usr/local/bin/parallel [05:10:49] Found freebayes - /usr/local/bin/freebayes [05:10:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:10:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:10:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:10:49] Found vcfuniq - /usr/local/bin/vcfuniq [05:10:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:10:49] Found gzip - /bin/gzip [05:10:49] Found vt - /usr/local/bin/vt [05:10:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:10:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:10:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:10:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:10:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:10:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:10:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:10:50] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:10:51] This is snippy 4.6.0
Show full stderr[05:10:51] This is snippy 4.6.0 [05:10:51] Written by Torsten Seemann [05:10:51] Obtained from https://github.com/tseemann/snippy [05:10:51] Detected operating system: linux [05:10:51] Enabling bundled linux tools. [05:10:51] Found bwa - /usr/local/bin/bwa [05:10:51] Found bcftools - /usr/local/bin/bcftools [05:10:51] Found samtools - /usr/local/bin/samtools [05:10:51] Found java - /usr/local/bin/java [05:10:51] Found snpEff - /usr/local/bin/snpEff [05:10:51] Found samclip - /usr/local/bin/samclip [05:10:51] Found seqtk - /usr/local/bin/seqtk [05:10:51] Found parallel - /usr/local/bin/parallel [05:10:51] Found freebayes - /usr/local/bin/freebayes [05:10:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:10:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:10:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:10:51] Found vcfuniq - /usr/local/bin/vcfuniq [05:10:51] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:10:51] Found gzip - /bin/gzip [05:10:51] Found vt - /usr/local/bin/vt [05:10:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:10:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:10:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:10:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:10:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:10:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:10:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:10:53] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:05:21] This is snippy 4.6.0
Show full stderr[05:05:21] This is snippy 4.6.0 [05:05:21] Written by Torsten Seemann [05:05:21] Obtained from https://github.com/tseemann/snippy [05:05:21] Detected operating system: linux [05:05:21] Enabling bundled linux tools. [05:05:21] Found bwa - /usr/local/bin/bwa [05:05:21] Found bcftools - /usr/local/bin/bcftools [05:05:21] Found samtools - /usr/local/bin/samtools [05:05:21] Found java - /usr/local/bin/java [05:05:21] Found snpEff - /usr/local/bin/snpEff [05:05:21] Found samclip - /usr/local/bin/samclip [05:05:21] Found seqtk - /usr/local/bin/seqtk [05:05:21] Found parallel - /usr/local/bin/parallel [05:05:21] Found freebayes - /usr/local/bin/freebayes [05:05:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:05:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:05:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:05:21] Found vcfuniq - /usr/local/bin/vcfuniq [05:05:21] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:05:21] Found gzip - /bin/gzip [05:05:21] Found vt - /usr/local/bin/vt [05:05:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:05:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:05:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:05:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:05:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:05:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:05:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:05:21] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:05:33] This is snippy 4.6.0
Show full stderr[05:05:33] This is snippy 4.6.0 [05:05:33] Written by Torsten Seemann [05:05:33] Obtained from https://github.com/tseemann/snippy [05:05:33] Detected operating system: linux [05:05:33] Enabling bundled linux tools. [05:05:33] Found bwa - /usr/local/bin/bwa [05:05:33] Found bcftools - /usr/local/bin/bcftools [05:05:33] Found samtools - /usr/local/bin/samtools [05:05:33] Found java - /usr/local/bin/java [05:05:33] Found snpEff - /usr/local/bin/snpEff [05:05:33] Found samclip - /usr/local/bin/samclip [05:05:33] Found seqtk - /usr/local/bin/seqtk [05:05:33] Found parallel - /usr/local/bin/parallel [05:05:33] Found freebayes - /usr/local/bin/freebayes [05:05:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:05:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:05:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:05:33] Found vcfuniq - /usr/local/bin/vcfuniq [05:05:33] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:05:33] Found gzip - /bin/gzip [05:05:33] Found vt - /usr/local/bin/vt [05:05:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:05:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:05:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:05:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:05:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:05:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:05:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:05:34] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:09:42] This is snippy 4.6.0
Show full stderr[05:09:42] This is snippy 4.6.0 [05:09:42] Written by Torsten Seemann [05:09:42] Obtained from https://github.com/tseemann/snippy [05:09:42] Detected operating system: linux [05:09:42] Enabling bundled linux tools. [05:09:42] Found bwa - /usr/local/bin/bwa [05:09:42] Found bcftools - /usr/local/bin/bcftools [05:09:42] Found samtools - /usr/local/bin/samtools [05:09:42] Found java - /usr/local/bin/java [05:09:42] Found snpEff - /usr/local/bin/snpEff [05:09:42] Found samclip - /usr/local/bin/samclip [05:09:42] Found seqtk - /usr/local/bin/seqtk [05:09:42] Found parallel - /usr/local/bin/parallel [05:09:42] Found freebayes - /usr/local/bin/freebayes [05:09:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:09:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:09:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:09:42] Found vcfuniq - /usr/local/bin/vcfuniq [05:09:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:09:42] Found gzip - /bin/gzip [05:09:42] Found vt - /usr/local/bin/vt [05:09:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:09:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:09:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:09:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:09:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:09:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:09:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:09:43] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:05:15] This is snippy 4.6.0
Show full stderr[05:05:15] This is snippy 4.6.0 [05:05:15] Written by Torsten Seemann [05:05:15] Obtained from https://github.com/tseemann/snippy [05:05:15] Detected operating system: linux [05:05:15] Enabling bundled linux tools. [05:05:15] Found bwa - /usr/local/bin/bwa [05:05:15] Found bcftools - /usr/local/bin/bcftools [05:05:15] Found samtools - /usr/local/bin/samtools [05:05:15] Found java - /usr/local/bin/java [05:05:15] Found snpEff - /usr/local/bin/snpEff [05:05:15] Found samclip - /usr/local/bin/samclip [05:05:15] Found seqtk - /usr/local/bin/seqtk [05:05:15] Found parallel - /usr/local/bin/parallel [05:05:15] Found freebayes - /usr/local/bin/freebayes [05:05:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:05:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:05:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:05:15] Found vcfuniq - /usr/local/bin/vcfuniq [05:05:15] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:05:15] Found gzip - /bin/gzip [05:05:15] Found vt - /usr/local/bin/vt [05:05:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:05:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:05:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:05:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:05:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:05:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:05:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:05:16] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:05:48] This is snippy 4.6.0
Show full stderr[05:05:48] This is snippy 4.6.0 [05:05:48] Written by Torsten Seemann [05:05:48] Obtained from https://github.com/tseemann/snippy [05:05:48] Detected operating system: linux [05:05:48] Enabling bundled linux tools. [05:05:48] Found bwa - /usr/local/bin/bwa [05:05:48] Found bcftools - /usr/local/bin/bcftools [05:05:48] Found samtools - /usr/local/bin/samtools [05:05:48] Found java - /usr/local/bin/java [05:05:48] Found snpEff - /usr/local/bin/snpEff [05:05:48] Found samclip - /usr/local/bin/samclip [05:05:48] Found seqtk - /usr/local/bin/seqtk [05:05:48] Found parallel - /usr/local/bin/parallel [05:05:48] Found freebayes - /usr/local/bin/freebayes [05:05:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:05:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:05:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:05:48] Found vcfuniq - /usr/local/bin/vcfuniq [05:05:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:05:48] Found gzip - /bin/gzip [05:05:48] Found vt - /usr/local/bin/vt [05:05:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:05:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:05:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:05:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:05:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:05:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:05:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:05:49] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:06:18] This is snippy 4.6.0
Show full stderr[05:06:18] This is snippy 4.6.0 [05:06:18] Written by Torsten Seemann [05:06:18] Obtained from https://github.com/tseemann/snippy [05:06:18] Detected operating system: linux [05:06:18] Enabling bundled linux tools. [05:06:18] Found bwa - /usr/local/bin/bwa [05:06:18] Found bcftools - /usr/local/bin/bcftools [05:06:18] Found samtools - /usr/local/bin/samtools [05:06:18] Found java - /usr/local/bin/java [05:06:18] Found snpEff - /usr/local/bin/snpEff [05:06:18] Found samclip - /usr/local/bin/samclip [05:06:18] Found seqtk - /usr/local/bin/seqtk [05:06:18] Found parallel - /usr/local/bin/parallel [05:06:18] Found freebayes - /usr/local/bin/freebayes [05:06:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:06:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:06:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:06:18] Found vcfuniq - /usr/local/bin/vcfuniq [05:06:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:06:18] Found gzip - /bin/gzip [05:06:18] Found vt - /usr/local/bin/vt [05:06:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:06:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:06:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:06:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:06:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:06:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:06:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:06:19] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:07:15] This is snippy 4.6.0
Show full stderr[05:07:15] This is snippy 4.6.0 [05:07:15] Written by Torsten Seemann [05:07:15] Obtained from https://github.com/tseemann/snippy [05:07:15] Detected operating system: linux [05:07:15] Enabling bundled linux tools. [05:07:15] Found bwa - /usr/local/bin/bwa [05:07:15] Found bcftools - /usr/local/bin/bcftools [05:07:15] Found samtools - /usr/local/bin/samtools [05:07:15] Found java - /usr/local/bin/java [05:07:15] Found snpEff - /usr/local/bin/snpEff [05:07:15] Found samclip - /usr/local/bin/samclip [05:07:15] Found seqtk - /usr/local/bin/seqtk [05:07:15] Found parallel - /usr/local/bin/parallel [05:07:15] Found freebayes - /usr/local/bin/freebayes [05:07:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:07:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:07:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:07:15] Found vcfuniq - /usr/local/bin/vcfuniq [05:07:15] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:07:15] Found gzip - /bin/gzip [05:07:15] Found vt - /usr/local/bin/vt [05:07:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:07:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:07:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:07:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:07:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:07:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:07:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:07:16] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:07:24] This is snippy 4.6.0
Show full stderr[05:07:24] This is snippy 4.6.0 [05:07:24] Written by Torsten Seemann [05:07:24] Obtained from https://github.com/tseemann/snippy [05:07:24] Detected operating system: linux [05:07:24] Enabling bundled linux tools. [05:07:24] Found bwa - /usr/local/bin/bwa [05:07:24] Found bcftools - /usr/local/bin/bcftools [05:07:24] Found samtools - /usr/local/bin/samtools [05:07:24] Found java - /usr/local/bin/java [05:07:24] Found snpEff - /usr/local/bin/snpEff [05:07:24] Found samclip - /usr/local/bin/samclip [05:07:24] Found seqtk - /usr/local/bin/seqtk [05:07:24] Found parallel - /usr/local/bin/parallel [05:07:24] Found freebayes - /usr/local/bin/freebayes [05:07:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:07:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:07:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:07:24] Found vcfuniq - /usr/local/bin/vcfuniq [05:07:24] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:07:24] Found gzip - /bin/gzip [05:07:24] Found vt - /usr/local/bin/vt [05:07:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:07:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:07:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:07:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:07:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:07:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:07:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:07:25] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:07:27] This is snippy 4.6.0
Show full stderr[05:07:27] This is snippy 4.6.0 [05:07:27] Written by Torsten Seemann [05:07:27] Obtained from https://github.com/tseemann/snippy [05:07:27] Detected operating system: linux [05:07:27] Enabling bundled linux tools. [05:07:27] Found bwa - /usr/local/bin/bwa [05:07:27] Found bcftools - /usr/local/bin/bcftools [05:07:27] Found samtools - /usr/local/bin/samtools [05:07:27] Found java - /usr/local/bin/java [05:07:27] Found snpEff - /usr/local/bin/snpEff [05:07:27] Found samclip - /usr/local/bin/samclip [05:07:27] Found seqtk - /usr/local/bin/seqtk [05:07:27] Found parallel - /usr/local/bin/parallel [05:07:27] Found freebayes - /usr/local/bin/freebayes [05:07:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:07:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:07:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:07:27] Found vcfuniq - /usr/local/bin/vcfuniq [05:07:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:07:27] Found gzip - /bin/gzip [05:07:27] Found vt - /usr/local/bin/vt [05:07:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:07:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:07:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:07:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:07:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:07:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:07:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:07:28] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:07:39] This is snippy 4.6.0
Show full stderr[05:07:39] This is snippy 4.6.0 [05:07:39] Written by Torsten Seemann [05:07:39] Obtained from https://github.com/tseemann/snippy [05:07:39] Detected operating system: linux [05:07:39] Enabling bundled linux tools. [05:07:39] Found bwa - /usr/local/bin/bwa [05:07:39] Found bcftools - /usr/local/bin/bcftools [05:07:39] Found samtools - /usr/local/bin/samtools [05:07:39] Found java - /usr/local/bin/java [05:07:39] Found snpEff - /usr/local/bin/snpEff [05:07:39] Found samclip - /usr/local/bin/samclip [05:07:39] Found seqtk - /usr/local/bin/seqtk [05:07:39] Found parallel - /usr/local/bin/parallel [05:07:39] Found freebayes - /usr/local/bin/freebayes [05:07:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:07:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:07:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:07:39] Found vcfuniq - /usr/local/bin/vcfuniq [05:07:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:07:39] Found gzip - /bin/gzip [05:07:39] Found vt - /usr/local/bin/vt [05:07:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:07:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:07:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:07:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:07:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:07:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:07:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:07:40] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:09:45] This is snippy 4.6.0
Show full stderr[05:09:45] This is snippy 4.6.0 [05:09:45] Written by Torsten Seemann [05:09:45] Obtained from https://github.com/tseemann/snippy [05:09:45] Detected operating system: linux [05:09:45] Enabling bundled linux tools. [05:09:45] Found bwa - /usr/local/bin/bwa [05:09:45] Found bcftools - /usr/local/bin/bcftools [05:09:45] Found samtools - /usr/local/bin/samtools [05:09:45] Found java - /usr/local/bin/java [05:09:45] Found snpEff - /usr/local/bin/snpEff [05:09:45] Found samclip - /usr/local/bin/samclip [05:09:45] Found seqtk - /usr/local/bin/seqtk [05:09:45] Found parallel - /usr/local/bin/parallel [05:09:45] Found freebayes - /usr/local/bin/freebayes [05:09:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:09:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:09:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:09:45] Found vcfuniq - /usr/local/bin/vcfuniq [05:09:45] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:09:45] Found gzip - /bin/gzip [05:09:45] Found vt - /usr/local/bin/vt [05:09:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:09:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:09:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:09:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:09:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:09:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:09:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:09:46] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:09:57] This is snippy 4.6.0
Show full stderr[05:09:57] This is snippy 4.6.0 [05:09:57] Written by Torsten Seemann [05:09:57] Obtained from https://github.com/tseemann/snippy [05:09:57] Detected operating system: linux [05:09:57] Enabling bundled linux tools. [05:09:57] Found bwa - /usr/local/bin/bwa [05:09:57] Found bcftools - /usr/local/bin/bcftools [05:09:57] Found samtools - /usr/local/bin/samtools [05:09:57] Found java - /usr/local/bin/java [05:09:57] Found snpEff - /usr/local/bin/snpEff [05:09:57] Found samclip - /usr/local/bin/samclip [05:09:57] Found seqtk - /usr/local/bin/seqtk [05:09:57] Found parallel - /usr/local/bin/parallel [05:09:57] Found freebayes - /usr/local/bin/freebayes [05:09:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:09:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:09:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:09:57] Found vcfuniq - /usr/local/bin/vcfuniq [05:09:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:09:57] Found gzip - /bin/gzip [05:09:57] Found vt - /usr/local/bin/vt [05:09:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:09:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:09:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:09:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:09:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:09:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:09:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:09:58] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:10:00] This is snippy 4.6.0
Show full stderr[05:10:00] This is snippy 4.6.0 [05:10:00] Written by Torsten Seemann [05:10:00] Obtained from https://github.com/tseemann/snippy [05:10:00] Detected operating system: linux [05:10:00] Enabling bundled linux tools. [05:10:00] Found bwa - /usr/local/bin/bwa [05:10:00] Found bcftools - /usr/local/bin/bcftools [05:10:00] Found samtools - /usr/local/bin/samtools [05:10:00] Found java - /usr/local/bin/java [05:10:00] Found snpEff - /usr/local/bin/snpEff [05:10:00] Found samclip - /usr/local/bin/samclip [05:10:00] Found seqtk - /usr/local/bin/seqtk [05:10:00] Found parallel - /usr/local/bin/parallel [05:10:00] Found freebayes - /usr/local/bin/freebayes [05:10:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:10:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:10:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:10:00] Found vcfuniq - /usr/local/bin/vcfuniq [05:10:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:10:00] Found gzip - /bin/gzip [05:10:00] Found vt - /usr/local/bin/vt [05:10:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:10:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:10:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:10:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:10:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:10:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:10:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:10:01] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:10:06] This is snippy 4.6.0
Show full stderr[05:10:06] This is snippy 4.6.0 [05:10:06] Written by Torsten Seemann [05:10:06] Obtained from https://github.com/tseemann/snippy [05:10:06] Detected operating system: linux [05:10:06] Enabling bundled linux tools. [05:10:06] Found bwa - /usr/local/bin/bwa [05:10:06] Found bcftools - /usr/local/bin/bcftools [05:10:06] Found samtools - /usr/local/bin/samtools [05:10:06] Found java - /usr/local/bin/java [05:10:06] Found snpEff - /usr/local/bin/snpEff [05:10:06] Found samclip - /usr/local/bin/samclip [05:10:06] Found seqtk - /usr/local/bin/seqtk [05:10:06] Found parallel - /usr/local/bin/parallel [05:10:06] Found freebayes - /usr/local/bin/freebayes [05:10:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:10:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:10:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:10:06] Found vcfuniq - /usr/local/bin/vcfuniq [05:10:06] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:10:06] Found gzip - /bin/gzip [05:10:06] Found vt - /usr/local/bin/vt [05:10:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:10:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:10:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:10:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:10:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:10:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:10:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:10:08] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:10:12] This is snippy 4.6.0
Show full stderr[05:10:12] This is snippy 4.6.0 [05:10:12] Written by Torsten Seemann [05:10:12] Obtained from https://github.com/tseemann/snippy [05:10:12] Detected operating system: linux [05:10:12] Enabling bundled linux tools. [05:10:12] Found bwa - /usr/local/bin/bwa [05:10:12] Found bcftools - /usr/local/bin/bcftools [05:10:12] Found samtools - /usr/local/bin/samtools [05:10:12] Found java - /usr/local/bin/java [05:10:12] Found snpEff - /usr/local/bin/snpEff [05:10:12] Found samclip - /usr/local/bin/samclip [05:10:12] Found seqtk - /usr/local/bin/seqtk [05:10:12] Found parallel - /usr/local/bin/parallel [05:10:12] Found freebayes - /usr/local/bin/freebayes [05:10:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:10:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:10:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:10:12] Found vcfuniq - /usr/local/bin/vcfuniq [05:10:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:10:12] Found gzip - /bin/gzip [05:10:12] Found vt - /usr/local/bin/vt [05:10:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:10:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:10:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:10:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:10:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:10:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:10:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:10:13] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:10:15] This is snippy 4.6.0
Show full stderr[05:10:15] This is snippy 4.6.0 [05:10:15] Written by Torsten Seemann [05:10:15] Obtained from https://github.com/tseemann/snippy [05:10:15] Detected operating system: linux [05:10:15] Enabling bundled linux tools. [05:10:15] Found bwa - /usr/local/bin/bwa [05:10:15] Found bcftools - /usr/local/bin/bcftools [05:10:15] Found samtools - /usr/local/bin/samtools [05:10:15] Found java - /usr/local/bin/java [05:10:15] Found snpEff - /usr/local/bin/snpEff [05:10:15] Found samclip - /usr/local/bin/samclip [05:10:15] Found seqtk - /usr/local/bin/seqtk [05:10:15] Found parallel - /usr/local/bin/parallel [05:10:15] Found freebayes - /usr/local/bin/freebayes [05:10:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:10:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:10:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:10:15] Found vcfuniq - /usr/local/bin/vcfuniq [05:10:15] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:10:15] Found gzip - /bin/gzip [05:10:15] Found vt - /usr/local/bin/vt [05:10:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:10:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:10:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:10:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:10:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:10:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:10:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:10:16] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:10:21] This is snippy 4.6.0
Show full stderr[05:10:21] This is snippy 4.6.0 [05:10:21] Written by Torsten Seemann [05:10:21] Obtained from https://github.com/tseemann/snippy [05:10:21] Detected operating system: linux [05:10:21] Enabling bundled linux tools. [05:10:21] Found bwa - /usr/local/bin/bwa [05:10:21] Found bcftools - /usr/local/bin/bcftools [05:10:21] Found samtools - /usr/local/bin/samtools [05:10:21] Found java - /usr/local/bin/java [05:10:21] Found snpEff - /usr/local/bin/snpEff [05:10:21] Found samclip - /usr/local/bin/samclip [05:10:21] Found seqtk - /usr/local/bin/seqtk [05:10:21] Found parallel - /usr/local/bin/parallel [05:10:21] Found freebayes - /usr/local/bin/freebayes [05:10:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:10:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:10:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:10:21] Found vcfuniq - /usr/local/bin/vcfuniq [05:10:21] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:10:21] Found gzip - /bin/gzip [05:10:21] Found vt - /usr/local/bin/vt [05:10:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:10:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:10:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:10:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:10:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:10:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:10:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:10:22] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:10:30] This is snippy 4.6.0
Show full stderr[05:10:30] This is snippy 4.6.0 [05:10:30] Written by Torsten Seemann [05:10:30] Obtained from https://github.com/tseemann/snippy [05:10:30] Detected operating system: linux [05:10:30] Enabling bundled linux tools. [05:10:30] Found bwa - /usr/local/bin/bwa [05:10:30] Found bcftools - /usr/local/bin/bcftools [05:10:30] Found samtools - /usr/local/bin/samtools [05:10:30] Found java - /usr/local/bin/java [05:10:30] Found snpEff - /usr/local/bin/snpEff [05:10:30] Found samclip - /usr/local/bin/samclip [05:10:30] Found seqtk - /usr/local/bin/seqtk [05:10:30] Found parallel - /usr/local/bin/parallel [05:10:30] Found freebayes - /usr/local/bin/freebayes [05:10:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:10:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:10:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:10:30] Found vcfuniq - /usr/local/bin/vcfuniq [05:10:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:10:30] Found gzip - /bin/gzip [05:10:30] Found vt - /usr/local/bin/vt [05:10:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:10:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:10:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:10:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:10:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:10:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:10:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:10:32] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:10:36] This is snippy 4.6.0
Show full stderr[05:10:36] This is snippy 4.6.0 [05:10:36] Written by Torsten Seemann [05:10:36] Obtained from https://github.com/tseemann/snippy [05:10:36] Detected operating system: linux [05:10:36] Enabling bundled linux tools. [05:10:36] Found bwa - /usr/local/bin/bwa [05:10:36] Found bcftools - /usr/local/bin/bcftools [05:10:36] Found samtools - /usr/local/bin/samtools [05:10:36] Found java - /usr/local/bin/java [05:10:36] Found snpEff - /usr/local/bin/snpEff [05:10:36] Found samclip - /usr/local/bin/samclip [05:10:36] Found seqtk - /usr/local/bin/seqtk [05:10:36] Found parallel - /usr/local/bin/parallel [05:10:36] Found freebayes - /usr/local/bin/freebayes [05:10:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:10:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:10:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:10:36] Found vcfuniq - /usr/local/bin/vcfuniq [05:10:36] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:10:36] Found gzip - /bin/gzip [05:10:36] Found vt - /usr/local/bin/vt [05:10:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:10:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:10:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:10:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:10:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:10:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:10:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:10:37] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:08:06] This is snippy 4.6.0
Show full stderr[05:08:06] This is snippy 4.6.0 [05:08:06] Written by Torsten Seemann [05:08:06] Obtained from https://github.com/tseemann/snippy [05:08:06] Detected operating system: linux [05:08:06] Enabling bundled linux tools. [05:08:06] Found bwa - /usr/local/bin/bwa [05:08:06] Found bcftools - /usr/local/bin/bcftools [05:08:06] Found samtools - /usr/local/bin/samtools [05:08:06] Found java - /usr/local/bin/java [05:08:06] Found snpEff - /usr/local/bin/snpEff [05:08:06] Found samclip - /usr/local/bin/samclip [05:08:06] Found seqtk - /usr/local/bin/seqtk [05:08:06] Found parallel - /usr/local/bin/parallel [05:08:06] Found freebayes - /usr/local/bin/freebayes [05:08:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:08:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:08:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:08:06] Found vcfuniq - /usr/local/bin/vcfuniq [05:08:06] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:08:06] Found gzip - /bin/gzip [05:08:06] Found vt - /usr/local/bin/vt [05:08:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:08:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:08:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:08:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:08:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:08:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:08:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:08:07] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:08:33] This is snippy 4.6.0
Show full stderr[05:08:33] This is snippy 4.6.0 [05:08:33] Written by Torsten Seemann [05:08:33] Obtained from https://github.com/tseemann/snippy [05:08:33] Detected operating system: linux [05:08:33] Enabling bundled linux tools. [05:08:33] Found bwa - /usr/local/bin/bwa [05:08:33] Found bcftools - /usr/local/bin/bcftools [05:08:33] Found samtools - /usr/local/bin/samtools [05:08:33] Found java - /usr/local/bin/java [05:08:33] Found snpEff - /usr/local/bin/snpEff [05:08:33] Found samclip - /usr/local/bin/samclip [05:08:33] Found seqtk - /usr/local/bin/seqtk [05:08:33] Found parallel - /usr/local/bin/parallel [05:08:33] Found freebayes - /usr/local/bin/freebayes [05:08:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:08:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:08:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:08:33] Found vcfuniq - /usr/local/bin/vcfuniq [05:08:33] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:08:33] Found gzip - /bin/gzip [05:08:33] Found vt - /usr/local/bin/vt [05:08:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:08:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:08:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:08:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:08:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:08:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:08:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:08:34] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:08:48] This is snippy 4.6.0
Show full stderr[05:08:48] This is snippy 4.6.0 [05:08:48] Written by Torsten Seemann [05:08:48] Obtained from https://github.com/tseemann/snippy [05:08:48] Detected operating system: linux [05:08:48] Enabling bundled linux tools. [05:08:48] Found bwa - /usr/local/bin/bwa [05:08:48] Found bcftools - /usr/local/bin/bcftools [05:08:48] Found samtools - /usr/local/bin/samtools [05:08:48] Found java - /usr/local/bin/java [05:08:48] Found snpEff - /usr/local/bin/snpEff [05:08:48] Found samclip - /usr/local/bin/samclip [05:08:48] Found seqtk - /usr/local/bin/seqtk [05:08:48] Found parallel - /usr/local/bin/parallel [05:08:48] Found freebayes - /usr/local/bin/freebayes [05:08:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:08:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:08:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:08:48] Found vcfuniq - /usr/local/bin/vcfuniq [05:08:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:08:48] Found gzip - /bin/gzip [05:08:48] Found vt - /usr/local/bin/vt [05:08:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:08:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:08:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:08:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:08:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:08:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:08:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:08:49] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:08:55] This is snippy 4.6.0
Show full stderr[05:08:55] This is snippy 4.6.0 [05:08:55] Written by Torsten Seemann [05:08:55] Obtained from https://github.com/tseemann/snippy [05:08:55] Detected operating system: linux [05:08:55] Enabling bundled linux tools. [05:08:55] Found bwa - /usr/local/bin/bwa [05:08:55] Found bcftools - /usr/local/bin/bcftools [05:08:55] Found samtools - /usr/local/bin/samtools [05:08:55] Found java - /usr/local/bin/java [05:08:55] Found snpEff - /usr/local/bin/snpEff [05:08:55] Found samclip - /usr/local/bin/samclip [05:08:55] Found seqtk - /usr/local/bin/seqtk [05:08:55] Found parallel - /usr/local/bin/parallel [05:08:55] Found freebayes - /usr/local/bin/freebayes [05:08:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:08:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:08:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:08:55] Found vcfuniq - /usr/local/bin/vcfuniq [05:08:55] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:08:55] Found gzip - /bin/gzip [05:08:55] Found vt - /usr/local/bin/vt [05:08:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:08:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:08:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:08:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:08:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:08:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:08:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:08:56] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:09:00] This is snippy 4.6.0
Show full stderr[05:09:00] This is snippy 4.6.0 [05:09:00] Written by Torsten Seemann [05:09:00] Obtained from https://github.com/tseemann/snippy [05:09:00] Detected operating system: linux [05:09:00] Enabling bundled linux tools. [05:09:00] Found bwa - /usr/local/bin/bwa [05:09:00] Found bcftools - /usr/local/bin/bcftools [05:09:00] Found samtools - /usr/local/bin/samtools [05:09:00] Found java - /usr/local/bin/java [05:09:00] Found snpEff - /usr/local/bin/snpEff [05:09:00] Found samclip - /usr/local/bin/samclip [05:09:00] Found seqtk - /usr/local/bin/seqtk [05:09:00] Found parallel - /usr/local/bin/parallel [05:09:00] Found freebayes - /usr/local/bin/freebayes [05:09:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:09:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:09:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:09:00] Found vcfuniq - /usr/local/bin/vcfuniq [05:09:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:09:00] Found gzip - /bin/gzip [05:09:00] Found vt - /usr/local/bin/vt [05:09:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:09:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:09:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:09:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:09:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:09:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:09:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:09:01] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:09:18] This is snippy 4.6.0
Show full stderr[05:09:18] This is snippy 4.6.0 [05:09:18] Written by Torsten Seemann [05:09:18] Obtained from https://github.com/tseemann/snippy [05:09:18] Detected operating system: linux [05:09:18] Enabling bundled linux tools. [05:09:18] Found bwa - /usr/local/bin/bwa [05:09:18] Found bcftools - /usr/local/bin/bcftools [05:09:18] Found samtools - /usr/local/bin/samtools [05:09:18] Found java - /usr/local/bin/java [05:09:18] Found snpEff - /usr/local/bin/snpEff [05:09:18] Found samclip - /usr/local/bin/samclip [05:09:18] Found seqtk - /usr/local/bin/seqtk [05:09:18] Found parallel - /usr/local/bin/parallel [05:09:18] Found freebayes - /usr/local/bin/freebayes [05:09:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:09:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:09:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:09:18] Found vcfuniq - /usr/local/bin/vcfuniq [05:09:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:09:18] Found gzip - /bin/gzip [05:09:18] Found vt - /usr/local/bin/vt [05:09:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:09:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:09:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:09:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:09:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:09:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:09:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:09:19] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:11:00] This is snippy 4.6.0
Show full stderr[05:11:00] This is snippy 4.6.0 [05:11:00] Written by Torsten Seemann [05:11:00] Obtained from https://github.com/tseemann/snippy [05:11:00] Detected operating system: linux [05:11:00] Enabling bundled linux tools. [05:11:00] Found bwa - /usr/local/bin/bwa [05:11:00] Found bcftools - /usr/local/bin/bcftools [05:11:00] Found samtools - /usr/local/bin/samtools [05:11:00] Found java - /usr/local/bin/java [05:11:00] Found snpEff - /usr/local/bin/snpEff [05:11:00] Found samclip - /usr/local/bin/samclip [05:11:00] Found seqtk - /usr/local/bin/seqtk [05:11:00] Found parallel - /usr/local/bin/parallel [05:11:00] Found freebayes - /usr/local/bin/freebayes [05:11:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:11:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:11:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:11:00] Found vcfuniq - /usr/local/bin/vcfuniq [05:11:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:11:00] Found gzip - /bin/gzip [05:11:00] Found vt - /usr/local/bin/vt [05:11:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:11:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:11:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:11:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:11:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:11:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:11:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:11:01] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:11:03] This is snippy 4.6.0
Show full stderr[05:11:03] This is snippy 4.6.0 [05:11:03] Written by Torsten Seemann [05:11:03] Obtained from https://github.com/tseemann/snippy [05:11:03] Detected operating system: linux [05:11:03] Enabling bundled linux tools. [05:11:03] Found bwa - /usr/local/bin/bwa [05:11:03] Found bcftools - /usr/local/bin/bcftools [05:11:03] Found samtools - /usr/local/bin/samtools [05:11:03] Found java - /usr/local/bin/java [05:11:03] Found snpEff - /usr/local/bin/snpEff [05:11:03] Found samclip - /usr/local/bin/samclip [05:11:04] Found seqtk - /usr/local/bin/seqtk [05:11:04] Found parallel - /usr/local/bin/parallel [05:11:04] Found freebayes - /usr/local/bin/freebayes [05:11:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:11:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:11:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:11:04] Found vcfuniq - /usr/local/bin/vcfuniq [05:11:04] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:11:04] Found gzip - /bin/gzip [05:11:04] Found vt - /usr/local/bin/vt [05:11:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:11:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:11:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:11:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:11:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:11:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:11:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:11:05] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:11:12] This is snippy 4.6.0
Show full stderr[05:11:12] This is snippy 4.6.0 [05:11:12] Written by Torsten Seemann [05:11:12] Obtained from https://github.com/tseemann/snippy [05:11:12] Detected operating system: linux [05:11:12] Enabling bundled linux tools. [05:11:12] Found bwa - /usr/local/bin/bwa [05:11:12] Found bcftools - /usr/local/bin/bcftools [05:11:12] Found samtools - /usr/local/bin/samtools [05:11:12] Found java - /usr/local/bin/java [05:11:12] Found snpEff - /usr/local/bin/snpEff [05:11:12] Found samclip - /usr/local/bin/samclip [05:11:12] Found seqtk - /usr/local/bin/seqtk [05:11:12] Found parallel - /usr/local/bin/parallel [05:11:12] Found freebayes - /usr/local/bin/freebayes [05:11:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:11:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:11:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:11:12] Found vcfuniq - /usr/local/bin/vcfuniq [05:11:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:11:12] Found gzip - /bin/gzip [05:11:12] Found vt - /usr/local/bin/vt [05:11:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:11:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:11:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:11:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:11:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:11:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:11:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:11:14] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:11:16] This is snippy 4.6.0
Show full stderr[05:11:16] This is snippy 4.6.0 [05:11:16] Written by Torsten Seemann [05:11:16] Obtained from https://github.com/tseemann/snippy [05:11:16] Detected operating system: linux [05:11:16] Enabling bundled linux tools. [05:11:16] Found bwa - /usr/local/bin/bwa [05:11:16] Found bcftools - /usr/local/bin/bcftools [05:11:16] Found samtools - /usr/local/bin/samtools [05:11:16] Found java - /usr/local/bin/java [05:11:16] Found snpEff - /usr/local/bin/snpEff [05:11:16] Found samclip - /usr/local/bin/samclip [05:11:16] Found seqtk - /usr/local/bin/seqtk [05:11:16] Found parallel - /usr/local/bin/parallel [05:11:16] Found freebayes - /usr/local/bin/freebayes [05:11:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:11:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:11:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:11:16] Found vcfuniq - /usr/local/bin/vcfuniq [05:11:16] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:11:16] Found gzip - /bin/gzip [05:11:16] Found vt - /usr/local/bin/vt [05:11:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:11:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:11:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:11:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:11:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:11:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:11:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:11:16] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:11:21] This is snippy 4.6.0
Show full stderr[05:11:21] This is snippy 4.6.0 [05:11:21] Written by Torsten Seemann [05:11:21] Obtained from https://github.com/tseemann/snippy [05:11:21] Detected operating system: linux [05:11:21] Enabling bundled linux tools. [05:11:21] Found bwa - /usr/local/bin/bwa [05:11:21] Found bcftools - /usr/local/bin/bcftools [05:11:21] Found samtools - /usr/local/bin/samtools [05:11:21] Found java - /usr/local/bin/java [05:11:21] Found snpEff - /usr/local/bin/snpEff [05:11:21] Found samclip - /usr/local/bin/samclip [05:11:21] Found seqtk - /usr/local/bin/seqtk [05:11:21] Found parallel - /usr/local/bin/parallel [05:11:21] Found freebayes - /usr/local/bin/freebayes [05:11:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:11:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:11:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:11:21] Found vcfuniq - /usr/local/bin/vcfuniq [05:11:21] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:11:21] Found gzip - /bin/gzip [05:11:21] Found vt - /usr/local/bin/vt [05:11:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:11:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:11:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:11:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:11:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:11:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:11:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:11:22] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:11:39] This is snippy 4.6.0
Show full stderr[05:11:39] This is snippy 4.6.0 [05:11:39] Written by Torsten Seemann [05:11:39] Obtained from https://github.com/tseemann/snippy [05:11:39] Detected operating system: linux [05:11:39] Enabling bundled linux tools. [05:11:39] Found bwa - /usr/local/bin/bwa [05:11:39] Found bcftools - /usr/local/bin/bcftools [05:11:39] Found samtools - /usr/local/bin/samtools [05:11:39] Found java - /usr/local/bin/java [05:11:39] Found snpEff - /usr/local/bin/snpEff [05:11:39] Found samclip - /usr/local/bin/samclip [05:11:39] Found seqtk - /usr/local/bin/seqtk [05:11:39] Found parallel - /usr/local/bin/parallel [05:11:39] Found freebayes - /usr/local/bin/freebayes [05:11:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:11:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:11:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:11:39] Found vcfuniq - /usr/local/bin/vcfuniq [05:11:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:11:39] Found gzip - /bin/gzip [05:11:39] Found vt - /usr/local/bin/vt [05:11:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:11:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:11:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:11:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:11:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:11:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:11:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:11:40] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:08:18] This is snippy 4.6.0
Show full stderr[05:08:18] This is snippy 4.6.0 [05:08:18] Written by Torsten Seemann [05:08:18] Obtained from https://github.com/tseemann/snippy [05:08:18] Detected operating system: linux [05:08:18] Enabling bundled linux tools. [05:08:18] Found bwa - /usr/local/bin/bwa [05:08:18] Found bcftools - /usr/local/bin/bcftools [05:08:18] Found samtools - /usr/local/bin/samtools [05:08:18] Found java - /usr/local/bin/java [05:08:18] Found snpEff - /usr/local/bin/snpEff [05:08:18] Found samclip - /usr/local/bin/samclip [05:08:18] Found seqtk - /usr/local/bin/seqtk [05:08:18] Found parallel - /usr/local/bin/parallel [05:08:18] Found freebayes - /usr/local/bin/freebayes [05:08:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:08:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:08:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:08:18] Found vcfuniq - /usr/local/bin/vcfuniq [05:08:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:08:18] Found gzip - /bin/gzip [05:08:18] Found vt - /usr/local/bin/vt [05:08:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:08:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:08:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:08:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:08:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:08:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:08:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:08:19] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:08:30] This is snippy 4.6.0
Show full stderr[05:08:30] This is snippy 4.6.0 [05:08:30] Written by Torsten Seemann [05:08:30] Obtained from https://github.com/tseemann/snippy [05:08:30] Detected operating system: linux [05:08:30] Enabling bundled linux tools. [05:08:30] Found bwa - /usr/local/bin/bwa [05:08:30] Found bcftools - /usr/local/bin/bcftools [05:08:30] Found samtools - /usr/local/bin/samtools [05:08:30] Found java - /usr/local/bin/java [05:08:30] Found snpEff - /usr/local/bin/snpEff [05:08:30] Found samclip - /usr/local/bin/samclip [05:08:30] Found seqtk - /usr/local/bin/seqtk [05:08:30] Found parallel - /usr/local/bin/parallel [05:08:30] Found freebayes - /usr/local/bin/freebayes [05:08:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:08:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:08:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:08:30] Found vcfuniq - /usr/local/bin/vcfuniq [05:08:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:08:30] Found gzip - /bin/gzip [05:08:30] Found vt - /usr/local/bin/vt [05:08:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:08:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:08:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:08:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:08:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:08:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:08:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:08:31] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:08:45] This is snippy 4.6.0
Show full stderr[05:08:45] This is snippy 4.6.0 [05:08:45] Written by Torsten Seemann [05:08:45] Obtained from https://github.com/tseemann/snippy [05:08:45] Detected operating system: linux [05:08:45] Enabling bundled linux tools. [05:08:45] Found bwa - /usr/local/bin/bwa [05:08:45] Found bcftools - /usr/local/bin/bcftools [05:08:45] Found samtools - /usr/local/bin/samtools [05:08:45] Found java - /usr/local/bin/java [05:08:45] Found snpEff - /usr/local/bin/snpEff [05:08:45] Found samclip - /usr/local/bin/samclip [05:08:45] Found seqtk - /usr/local/bin/seqtk [05:08:45] Found parallel - /usr/local/bin/parallel [05:08:45] Found freebayes - /usr/local/bin/freebayes [05:08:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:08:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:08:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:08:45] Found vcfuniq - /usr/local/bin/vcfuniq [05:08:45] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:08:45] Found gzip - /bin/gzip [05:08:45] Found vt - /usr/local/bin/vt [05:08:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:08:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:08:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:08:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:08:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:08:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:08:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:08:46] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:09:03] This is snippy 4.6.0
Show full stderr[05:09:03] This is snippy 4.6.0 [05:09:03] Written by Torsten Seemann [05:09:03] Obtained from https://github.com/tseemann/snippy [05:09:03] Detected operating system: linux [05:09:03] Enabling bundled linux tools. [05:09:03] Found bwa - /usr/local/bin/bwa [05:09:03] Found bcftools - /usr/local/bin/bcftools [05:09:03] Found samtools - /usr/local/bin/samtools [05:09:03] Found java - /usr/local/bin/java [05:09:03] Found snpEff - /usr/local/bin/snpEff [05:09:03] Found samclip - /usr/local/bin/samclip [05:09:03] Found seqtk - /usr/local/bin/seqtk [05:09:03] Found parallel - /usr/local/bin/parallel [05:09:03] Found freebayes - /usr/local/bin/freebayes [05:09:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:09:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:09:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:09:03] Found vcfuniq - /usr/local/bin/vcfuniq [05:09:03] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:09:03] Found gzip - /bin/gzip [05:09:03] Found vt - /usr/local/bin/vt [05:09:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:09:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:09:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:09:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:09:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:09:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:09:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:09:04] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:09:33] This is snippy 4.6.0
Show full stderr[05:09:33] This is snippy 4.6.0 [05:09:33] Written by Torsten Seemann [05:09:33] Obtained from https://github.com/tseemann/snippy [05:09:33] Detected operating system: linux [05:09:33] Enabling bundled linux tools. [05:09:33] Found bwa - /usr/local/bin/bwa [05:09:33] Found bcftools - /usr/local/bin/bcftools [05:09:33] Found samtools - /usr/local/bin/samtools [05:09:33] Found java - /usr/local/bin/java [05:09:33] Found snpEff - /usr/local/bin/snpEff [05:09:33] Found samclip - /usr/local/bin/samclip [05:09:33] Found seqtk - /usr/local/bin/seqtk [05:09:33] Found parallel - /usr/local/bin/parallel [05:09:33] Found freebayes - /usr/local/bin/freebayes [05:09:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:09:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:09:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:09:33] Found vcfuniq - /usr/local/bin/vcfuniq [05:09:33] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:09:33] Found gzip - /bin/gzip [05:09:33] Found vt - /usr/local/bin/vt [05:09:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:09:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:09:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:09:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:09:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:09:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:09:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:09:34] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:10:39] This is snippy 4.6.0
Show full stderr[05:10:39] This is snippy 4.6.0 [05:10:39] Written by Torsten Seemann [05:10:39] Obtained from https://github.com/tseemann/snippy [05:10:39] Detected operating system: linux [05:10:39] Enabling bundled linux tools. [05:10:39] Found bwa - /usr/local/bin/bwa [05:10:39] Found bcftools - /usr/local/bin/bcftools [05:10:39] Found samtools - /usr/local/bin/samtools [05:10:39] Found java - /usr/local/bin/java [05:10:39] Found snpEff - /usr/local/bin/snpEff [05:10:39] Found samclip - /usr/local/bin/samclip [05:10:39] Found seqtk - /usr/local/bin/seqtk [05:10:39] Found parallel - /usr/local/bin/parallel [05:10:39] Found freebayes - /usr/local/bin/freebayes [05:10:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:10:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:10:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:10:39] Found vcfuniq - /usr/local/bin/vcfuniq [05:10:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:10:39] Found gzip - /bin/gzip [05:10:39] Found vt - /usr/local/bin/vt [05:10:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:10:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:10:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:10:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:10:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:10:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:10:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:10:40] Please supply a reference FASTA/GBK/EMBL file with --reference
1[09:51:55] This is snippy 4.6.0
Show full stderr[09:51:55] This is snippy 4.6.0 [09:51:55] Written by Torsten Seemann [09:51:55] Obtained from https://github.com/tseemann/snippy [09:51:55] Detected operating system: linux [09:51:55] Enabling bundled linux tools. [09:51:55] Found bwa - /usr/local/bin/bwa [09:51:55] Found bcftools - /usr/local/bin/bcftools [09:51:55] Found samtools - /usr/local/bin/samtools [09:51:55] Found java - /usr/local/bin/java [09:51:55] Found snpEff - /usr/local/bin/snpEff [09:51:55] Found samclip - /usr/local/bin/samclip [09:51:55] Found seqtk - /usr/local/bin/seqtk [09:51:55] Found parallel - /usr/local/bin/parallel [09:51:55] Found freebayes - /usr/local/bin/freebayes [09:51:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [09:51:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [09:51:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [09:51:55] Found vcfuniq - /usr/local/bin/vcfuniq [09:51:55] Found vcffirstheader - /usr/local/bin/vcffirstheader [09:51:55] Found gzip - /bin/gzip [09:51:55] Found vt - /usr/local/bin/vt [09:51:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [09:51:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [09:51:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [09:51:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [09:51:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [09:51:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [09:51:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [09:51:56] Please supply a reference FASTA/GBK/EMBL file with --reference
1[09:53:48] This is snippy 4.6.0
Show full stderr[09:53:48] This is snippy 4.6.0 [09:53:48] Written by Torsten Seemann [09:53:48] Obtained from https://github.com/tseemann/snippy [09:53:48] Detected operating system: linux [09:53:48] Enabling bundled linux tools. [09:53:48] Found bwa - /usr/local/bin/bwa [09:53:48] Found bcftools - /usr/local/bin/bcftools [09:53:48] Found samtools - /usr/local/bin/samtools [09:53:48] Found java - /usr/local/bin/java [09:53:48] Found snpEff - /usr/local/bin/snpEff [09:53:48] Found samclip - /usr/local/bin/samclip [09:53:48] Found seqtk - /usr/local/bin/seqtk [09:53:48] Found parallel - /usr/local/bin/parallel [09:53:48] Found freebayes - /usr/local/bin/freebayes [09:53:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [09:53:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [09:53:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [09:53:48] Found vcfuniq - /usr/local/bin/vcfuniq [09:53:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [09:53:48] Found gzip - /bin/gzip [09:53:48] Found vt - /usr/local/bin/vt [09:53:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [09:53:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [09:53:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [09:53:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [09:53:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [09:53:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [09:53:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [09:53:49] Please supply a reference FASTA/GBK/EMBL file with --reference
1[03:41:39] This is snippy 4.6.0
Show full stderr[03:41:39] This is snippy 4.6.0 [03:41:39] Written by Torsten Seemann [03:41:39] Obtained from https://github.com/tseemann/snippy [03:41:39] Detected operating system: linux [03:41:39] Enabling bundled linux tools. [03:41:39] Found bwa - /usr/local/bin/bwa [03:41:39] Found bcftools - /usr/local/bin/bcftools [03:41:39] Found samtools - /usr/local/bin/samtools [03:41:39] Found java - /usr/local/bin/java [03:41:39] Found snpEff - /usr/local/bin/snpEff [03:41:39] Found samclip - /usr/local/bin/samclip [03:41:39] Found seqtk - /usr/local/bin/seqtk [03:41:39] Found parallel - /usr/local/bin/parallel [03:41:39] Found freebayes - /usr/local/bin/freebayes [03:41:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:41:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:41:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:41:39] Found vcfuniq - /usr/local/bin/vcfuniq [03:41:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:41:39] Found gzip - /bin/gzip [03:41:39] Found vt - /usr/local/bin/vt [03:41:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:41:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:41:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:41:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:41:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:41:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:41:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:41:41] Please supply a reference FASTA/GBK/EMBL file with --reference
1[03:41:44] This is snippy 4.6.0
Show full stderr[03:41:44] This is snippy 4.6.0 [03:41:44] Written by Torsten Seemann [03:41:44] Obtained from https://github.com/tseemann/snippy [03:41:44] Detected operating system: linux [03:41:44] Enabling bundled linux tools. [03:41:44] Found bwa - /usr/local/bin/bwa [03:41:44] Found bcftools - /usr/local/bin/bcftools [03:41:44] Found samtools - /usr/local/bin/samtools [03:41:44] Found java - /usr/local/bin/java [03:41:44] Found snpEff - /usr/local/bin/snpEff [03:41:44] Found samclip - /usr/local/bin/samclip [03:41:44] Found seqtk - /usr/local/bin/seqtk [03:41:44] Found parallel - /usr/local/bin/parallel [03:41:44] Found freebayes - /usr/local/bin/freebayes [03:41:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:41:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:41:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:41:44] Found vcfuniq - /usr/local/bin/vcfuniq [03:41:44] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:41:44] Found gzip - /bin/gzip [03:41:44] Found vt - /usr/local/bin/vt [03:41:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:41:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:41:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:41:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:41:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:41:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:41:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:41:45] Please supply a reference FASTA/GBK/EMBL file with --reference
1[03:39:43] This is snippy 4.6.0
Show full stderr[03:39:43] This is snippy 4.6.0 [03:39:43] Written by Torsten Seemann [03:39:43] Obtained from https://github.com/tseemann/snippy [03:39:43] Detected operating system: linux [03:39:43] Enabling bundled linux tools. [03:39:43] Found bwa - /usr/local/bin/bwa [03:39:43] Found bcftools - /usr/local/bin/bcftools [03:39:43] Found samtools - /usr/local/bin/samtools [03:39:43] Found java - /usr/local/bin/java [03:39:43] Found snpEff - /usr/local/bin/snpEff [03:39:43] Found samclip - /usr/local/bin/samclip [03:39:43] Found seqtk - /usr/local/bin/seqtk [03:39:43] Found parallel - /usr/local/bin/parallel [03:39:43] Found freebayes - /usr/local/bin/freebayes [03:39:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:39:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:39:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:39:43] Found vcfuniq - /usr/local/bin/vcfuniq [03:39:43] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:39:43] Found gzip - /bin/gzip [03:39:43] Found vt - /usr/local/bin/vt [03:39:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:39:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:39:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:39:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:39:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:39:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:39:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:39:44] Please supply a reference FASTA/GBK/EMBL file with --reference
1[03:40:16] This is snippy 4.6.0
Show full stderr[03:40:16] This is snippy 4.6.0 [03:40:16] Written by Torsten Seemann [03:40:16] Obtained from https://github.com/tseemann/snippy [03:40:16] Detected operating system: linux [03:40:16] Enabling bundled linux tools. [03:40:16] Found bwa - /usr/local/bin/bwa [03:40:16] Found bcftools - /usr/local/bin/bcftools [03:40:16] Found samtools - /usr/local/bin/samtools [03:40:16] Found java - /usr/local/bin/java [03:40:16] Found snpEff - /usr/local/bin/snpEff [03:40:16] Found samclip - /usr/local/bin/samclip [03:40:16] Found seqtk - /usr/local/bin/seqtk [03:40:16] Found parallel - /usr/local/bin/parallel [03:40:16] Found freebayes - /usr/local/bin/freebayes [03:40:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:40:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:40:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:40:16] Found vcfuniq - /usr/local/bin/vcfuniq [03:40:16] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:40:16] Found gzip - /bin/gzip [03:40:16] Found vt - /usr/local/bin/vt [03:40:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:40:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:40:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:40:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:40:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:40:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:40:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:40:17] Please supply a reference FASTA/GBK/EMBL file with --reference
1[03:40:19] This is snippy 4.6.0
Show full stderr[03:40:19] This is snippy 4.6.0 [03:40:19] Written by Torsten Seemann [03:40:19] Obtained from https://github.com/tseemann/snippy [03:40:19] Detected operating system: linux [03:40:19] Enabling bundled linux tools. [03:40:19] Found bwa - /usr/local/bin/bwa [03:40:19] Found bcftools - /usr/local/bin/bcftools [03:40:19] Found samtools - /usr/local/bin/samtools [03:40:19] Found java - /usr/local/bin/java [03:40:19] Found snpEff - /usr/local/bin/snpEff [03:40:19] Found samclip - /usr/local/bin/samclip [03:40:19] Found seqtk - /usr/local/bin/seqtk [03:40:19] Found parallel - /usr/local/bin/parallel [03:40:19] Found freebayes - /usr/local/bin/freebayes [03:40:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:40:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:40:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:40:19] Found vcfuniq - /usr/local/bin/vcfuniq [03:40:19] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:40:19] Found gzip - /bin/gzip [03:40:19] Found vt - /usr/local/bin/vt [03:40:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:40:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:40:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:40:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:40:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:40:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:40:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:40:20] Please supply a reference FASTA/GBK/EMBL file with --reference
1[03:40:31] This is snippy 4.6.0
Show full stderr[03:40:31] This is snippy 4.6.0 [03:40:31] Written by Torsten Seemann [03:40:31] Obtained from https://github.com/tseemann/snippy [03:40:31] Detected operating system: linux [03:40:31] Enabling bundled linux tools. [03:40:31] Found bwa - /usr/local/bin/bwa [03:40:31] Found bcftools - /usr/local/bin/bcftools [03:40:31] Found samtools - /usr/local/bin/samtools [03:40:31] Found java - /usr/local/bin/java [03:40:31] Found snpEff - /usr/local/bin/snpEff [03:40:31] Found samclip - /usr/local/bin/samclip [03:40:31] Found seqtk - /usr/local/bin/seqtk [03:40:31] Found parallel - /usr/local/bin/parallel [03:40:31] Found freebayes - /usr/local/bin/freebayes [03:40:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:40:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:40:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:40:31] Found vcfuniq - /usr/local/bin/vcfuniq [03:40:31] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:40:31] Found gzip - /bin/gzip [03:40:31] Found vt - /usr/local/bin/vt [03:40:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:40:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:40:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:40:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:40:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:40:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:40:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:40:32] Please supply a reference FASTA/GBK/EMBL file with --reference
1[03:40:52] This is snippy 4.6.0
Show full stderr[03:40:52] This is snippy 4.6.0 [03:40:52] Written by Torsten Seemann [03:40:52] Obtained from https://github.com/tseemann/snippy [03:40:52] Detected operating system: linux [03:40:52] Enabling bundled linux tools. [03:40:52] Found bwa - /usr/local/bin/bwa [03:40:52] Found bcftools - /usr/local/bin/bcftools [03:40:52] Found samtools - /usr/local/bin/samtools [03:40:52] Found java - /usr/local/bin/java [03:40:52] Found snpEff - /usr/local/bin/snpEff [03:40:52] Found samclip - /usr/local/bin/samclip [03:40:52] Found seqtk - /usr/local/bin/seqtk [03:40:52] Found parallel - /usr/local/bin/parallel [03:40:52] Found freebayes - /usr/local/bin/freebayes [03:40:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:40:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:40:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:40:52] Found vcfuniq - /usr/local/bin/vcfuniq [03:40:52] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:40:52] Found gzip - /bin/gzip [03:40:52] Found vt - /usr/local/bin/vt [03:40:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:40:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:40:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:40:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:40:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:40:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:40:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:40:53] Please supply a reference FASTA/GBK/EMBL file with --reference
1[03:41:30] This is snippy 4.6.0
Show full stderr[03:41:30] This is snippy 4.6.0 [03:41:30] Written by Torsten Seemann [03:41:30] Obtained from https://github.com/tseemann/snippy [03:41:30] Detected operating system: linux [03:41:30] Enabling bundled linux tools. [03:41:30] Found bwa - /usr/local/bin/bwa [03:41:30] Found bcftools - /usr/local/bin/bcftools [03:41:30] Found samtools - /usr/local/bin/samtools [03:41:30] Found java - /usr/local/bin/java [03:41:30] Found snpEff - /usr/local/bin/snpEff [03:41:30] Found samclip - /usr/local/bin/samclip [03:41:30] Found seqtk - /usr/local/bin/seqtk [03:41:30] Found parallel - /usr/local/bin/parallel [03:41:30] Found freebayes - /usr/local/bin/freebayes [03:41:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:41:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:41:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:41:30] Found vcfuniq - /usr/local/bin/vcfuniq [03:41:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:41:30] Found gzip - /bin/gzip [03:41:30] Found vt - /usr/local/bin/vt [03:41:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:41:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:41:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:41:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:41:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:41:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:41:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:41:31] Please supply a reference FASTA/GBK/EMBL file with --reference
1[03:39:44] This is snippy 4.6.0
Show full stderr[03:39:44] This is snippy 4.6.0 [03:39:44] Written by Torsten Seemann [03:39:44] Obtained from https://github.com/tseemann/snippy [03:39:44] Detected operating system: linux [03:39:44] Enabling bundled linux tools. [03:39:44] Found bwa - /usr/local/bin/bwa [03:39:44] Found bcftools - /usr/local/bin/bcftools [03:39:44] Found samtools - /usr/local/bin/samtools [03:39:44] Found java - /usr/local/bin/java [03:39:44] Found snpEff - /usr/local/bin/snpEff [03:39:44] Found samclip - /usr/local/bin/samclip [03:39:44] Found seqtk - /usr/local/bin/seqtk [03:39:44] Found parallel - /usr/local/bin/parallel [03:39:44] Found freebayes - /usr/local/bin/freebayes [03:39:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:39:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:39:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:39:44] Found vcfuniq - /usr/local/bin/vcfuniq [03:39:44] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:39:44] Found gzip - /bin/gzip [03:39:44] Found vt - /usr/local/bin/vt [03:39:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:39:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:39:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:39:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:39:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:39:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:39:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:39:45] Please supply a reference FASTA/GBK/EMBL file with --reference
1[03:39:59] This is snippy 4.6.0
Show full stderr[03:39:59] This is snippy 4.6.0 [03:39:59] Written by Torsten Seemann [03:39:59] Obtained from https://github.com/tseemann/snippy [03:39:59] Detected operating system: linux [03:39:59] Enabling bundled linux tools. [03:39:59] Found bwa - /usr/local/bin/bwa [03:39:59] Found bcftools - /usr/local/bin/bcftools [03:39:59] Found samtools - /usr/local/bin/samtools [03:39:59] Found java - /usr/local/bin/java [03:39:59] Found snpEff - /usr/local/bin/snpEff [03:39:59] Found samclip - /usr/local/bin/samclip [03:39:59] Found seqtk - /usr/local/bin/seqtk [03:39:59] Found parallel - /usr/local/bin/parallel [03:39:59] Found freebayes - /usr/local/bin/freebayes [03:39:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:39:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:39:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:39:59] Found vcfuniq - /usr/local/bin/vcfuniq [03:39:59] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:39:59] Found gzip - /bin/gzip [03:39:59] Found vt - /usr/local/bin/vt [03:39:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:39:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:39:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:39:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:39:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:40:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:40:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:40:00] Please supply a reference FASTA/GBK/EMBL file with --reference
1[03:40:02] This is snippy 4.6.0
Show full stderr[03:40:02] This is snippy 4.6.0 [03:40:02] Written by Torsten Seemann [03:40:02] Obtained from https://github.com/tseemann/snippy [03:40:02] Detected operating system: linux [03:40:02] Enabling bundled linux tools. [03:40:02] Found bwa - /usr/local/bin/bwa [03:40:02] Found bcftools - /usr/local/bin/bcftools [03:40:02] Found samtools - /usr/local/bin/samtools [03:40:02] Found java - /usr/local/bin/java [03:40:02] Found snpEff - /usr/local/bin/snpEff [03:40:02] Found samclip - /usr/local/bin/samclip [03:40:02] Found seqtk - /usr/local/bin/seqtk [03:40:02] Found parallel - /usr/local/bin/parallel [03:40:02] Found freebayes - /usr/local/bin/freebayes [03:40:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:40:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:40:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:40:02] Found vcfuniq - /usr/local/bin/vcfuniq [03:40:02] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:40:02] Found gzip - /bin/gzip [03:40:02] Found vt - /usr/local/bin/vt [03:40:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:40:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:40:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:40:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:40:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:40:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:40:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:40:03] Please supply a reference FASTA/GBK/EMBL file with --reference
1[03:40:14] This is snippy 4.6.0
Show full stderr[03:40:14] This is snippy 4.6.0 [03:40:14] Written by Torsten Seemann [03:40:14] Obtained from https://github.com/tseemann/snippy [03:40:14] Detected operating system: linux [03:40:14] Enabling bundled linux tools. [03:40:14] Found bwa - /usr/local/bin/bwa [03:40:14] Found bcftools - /usr/local/bin/bcftools [03:40:14] Found samtools - /usr/local/bin/samtools [03:40:14] Found java - /usr/local/bin/java [03:40:14] Found snpEff - /usr/local/bin/snpEff [03:40:14] Found samclip - /usr/local/bin/samclip [03:40:14] Found seqtk - /usr/local/bin/seqtk [03:40:14] Found parallel - /usr/local/bin/parallel [03:40:14] Found freebayes - /usr/local/bin/freebayes [03:40:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:40:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:40:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:40:14] Found vcfuniq - /usr/local/bin/vcfuniq [03:40:14] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:40:14] Found gzip - /bin/gzip [03:40:14] Found vt - /usr/local/bin/vt [03:40:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:40:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:40:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:40:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:40:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:40:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:40:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:40:15] Please supply a reference FASTA/GBK/EMBL file with --reference
1[03:40:59] This is snippy 4.6.0
Show full stderr[03:40:59] This is snippy 4.6.0 [03:40:59] Written by Torsten Seemann [03:40:59] Obtained from https://github.com/tseemann/snippy [03:40:59] Detected operating system: linux [03:40:59] Enabling bundled linux tools. [03:40:59] Found bwa - /usr/local/bin/bwa [03:40:59] Found bcftools - /usr/local/bin/bcftools [03:40:59] Found samtools - /usr/local/bin/samtools [03:40:59] Found java - /usr/local/bin/java [03:40:59] Found snpEff - /usr/local/bin/snpEff [03:40:59] Found samclip - /usr/local/bin/samclip [03:40:59] Found seqtk - /usr/local/bin/seqtk [03:40:59] Found parallel - /usr/local/bin/parallel [03:40:59] Found freebayes - /usr/local/bin/freebayes [03:40:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:40:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:40:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:40:59] Found vcfuniq - /usr/local/bin/vcfuniq [03:40:59] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:40:59] Found gzip - /bin/gzip [03:40:59] Found vt - /usr/local/bin/vt [03:40:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:40:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:40:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:40:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:40:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:41:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:41:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:41:00] Please supply a reference FASTA/GBK/EMBL file with --reference
1[03:42:59] This is snippy 4.6.0
Show full stderr[03:42:59] This is snippy 4.6.0 [03:42:59] Written by Torsten Seemann [03:42:59] Obtained from https://github.com/tseemann/snippy [03:42:59] Detected operating system: linux [03:42:59] Enabling bundled linux tools. [03:42:59] Found bwa - /usr/local/bin/bwa [03:42:59] Found bcftools - /usr/local/bin/bcftools [03:42:59] Found samtools - /usr/local/bin/samtools [03:42:59] Found java - /usr/local/bin/java [03:42:59] Found snpEff - /usr/local/bin/snpEff [03:42:59] Found samclip - /usr/local/bin/samclip [03:42:59] Found seqtk - /usr/local/bin/seqtk [03:42:59] Found parallel - /usr/local/bin/parallel [03:42:59] Found freebayes - /usr/local/bin/freebayes [03:42:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:42:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:42:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:42:59] Found vcfuniq - /usr/local/bin/vcfuniq [03:42:59] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:42:59] Found gzip - /bin/gzip [03:42:59] Found vt - /usr/local/bin/vt [03:42:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:42:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:42:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:42:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:42:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:43:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:43:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:43:00] Please supply a reference FASTA/GBK/EMBL file with --reference
1[03:42:25] This is snippy 4.6.0
Show full stderr[03:42:25] This is snippy 4.6.0 [03:42:25] Written by Torsten Seemann [03:42:25] Obtained from https://github.com/tseemann/snippy [03:42:25] Detected operating system: linux [03:42:25] Enabling bundled linux tools. [03:42:25] Found bwa - /usr/local/bin/bwa [03:42:25] Found bcftools - /usr/local/bin/bcftools [03:42:25] Found samtools - /usr/local/bin/samtools [03:42:25] Found java - /usr/local/bin/java [03:42:25] Found snpEff - /usr/local/bin/snpEff [03:42:25] Found samclip - /usr/local/bin/samclip [03:42:25] Found seqtk - /usr/local/bin/seqtk [03:42:25] Found parallel - /usr/local/bin/parallel [03:42:25] Found freebayes - /usr/local/bin/freebayes [03:42:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:42:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:42:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:42:25] Found vcfuniq - /usr/local/bin/vcfuniq [03:42:25] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:42:25] Found gzip - /bin/gzip [03:42:25] Found vt - /usr/local/bin/vt [03:42:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:42:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:42:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:42:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:42:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:42:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:42:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:42:26] Please supply a reference FASTA/GBK/EMBL file with --reference
1[03:42:32] This is snippy 4.6.0
Show full stderr[03:42:32] This is snippy 4.6.0 [03:42:32] Written by Torsten Seemann [03:42:32] Obtained from https://github.com/tseemann/snippy [03:42:32] Detected operating system: linux [03:42:32] Enabling bundled linux tools. [03:42:32] Found bwa - /usr/local/bin/bwa [03:42:32] Found bcftools - /usr/local/bin/bcftools [03:42:32] Found samtools - /usr/local/bin/samtools [03:42:32] Found java - /usr/local/bin/java [03:42:32] Found snpEff - /usr/local/bin/snpEff [03:42:32] Found samclip - /usr/local/bin/samclip [03:42:32] Found seqtk - /usr/local/bin/seqtk [03:42:32] Found parallel - /usr/local/bin/parallel [03:42:32] Found freebayes - /usr/local/bin/freebayes [03:42:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:42:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:42:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:42:32] Found vcfuniq - /usr/local/bin/vcfuniq [03:42:32] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:42:32] Found gzip - /bin/gzip [03:42:32] Found vt - /usr/local/bin/vt [03:42:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:42:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:42:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:42:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:42:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:42:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:42:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:42:34] Please supply a reference FASTA/GBK/EMBL file with --reference
1[03:42:41] This is snippy 4.6.0
Show full stderr[03:42:41] This is snippy 4.6.0 [03:42:41] Written by Torsten Seemann [03:42:41] Obtained from https://github.com/tseemann/snippy [03:42:41] Detected operating system: linux [03:42:41] Enabling bundled linux tools. [03:42:41] Found bwa - /usr/local/bin/bwa [03:42:41] Found bcftools - /usr/local/bin/bcftools [03:42:41] Found samtools - /usr/local/bin/samtools [03:42:41] Found java - /usr/local/bin/java [03:42:41] Found snpEff - /usr/local/bin/snpEff [03:42:41] Found samclip - /usr/local/bin/samclip [03:42:41] Found seqtk - /usr/local/bin/seqtk [03:42:41] Found parallel - /usr/local/bin/parallel [03:42:41] Found freebayes - /usr/local/bin/freebayes [03:42:41] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:42:41] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:42:41] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:42:41] Found vcfuniq - /usr/local/bin/vcfuniq [03:42:41] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:42:41] Found gzip - /bin/gzip [03:42:41] Found vt - /usr/local/bin/vt [03:42:41] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:42:41] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:42:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:42:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:42:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:42:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:42:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:42:42] Please supply a reference FASTA/GBK/EMBL file with --reference
1[03:43:13] This is snippy 4.6.0
Show full stderr[03:43:13] This is snippy 4.6.0 [03:43:13] Written by Torsten Seemann [03:43:13] Obtained from https://github.com/tseemann/snippy [03:43:13] Detected operating system: linux [03:43:13] Enabling bundled linux tools. [03:43:13] Found bwa - /usr/local/bin/bwa [03:43:13] Found bcftools - /usr/local/bin/bcftools [03:43:13] Found samtools - /usr/local/bin/samtools [03:43:13] Found java - /usr/local/bin/java [03:43:13] Found snpEff - /usr/local/bin/snpEff [03:43:13] Found samclip - /usr/local/bin/samclip [03:43:13] Found seqtk - /usr/local/bin/seqtk [03:43:13] Found parallel - /usr/local/bin/parallel [03:43:13] Found freebayes - /usr/local/bin/freebayes [03:43:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:43:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:43:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:43:13] Found vcfuniq - /usr/local/bin/vcfuniq [03:43:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:43:13] Found gzip - /bin/gzip [03:43:13] Found vt - /usr/local/bin/vt [03:43:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:43:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:43:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:43:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:43:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:43:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:43:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:43:15] Please supply a reference FASTA/GBK/EMBL file with --reference
1[03:43:19] This is snippy 4.6.0
Show full stderr[03:43:19] This is snippy 4.6.0 [03:43:19] Written by Torsten Seemann [03:43:19] Obtained from https://github.com/tseemann/snippy [03:43:19] Detected operating system: linux [03:43:19] Enabling bundled linux tools. [03:43:19] Found bwa - /usr/local/bin/bwa [03:43:19] Found bcftools - /usr/local/bin/bcftools [03:43:19] Found samtools - /usr/local/bin/samtools [03:43:19] Found java - /usr/local/bin/java [03:43:19] Found snpEff - /usr/local/bin/snpEff [03:43:19] Found samclip - /usr/local/bin/samclip [03:43:19] Found seqtk - /usr/local/bin/seqtk [03:43:19] Found parallel - /usr/local/bin/parallel [03:43:19] Found freebayes - /usr/local/bin/freebayes [03:43:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:43:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:43:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:43:19] Found vcfuniq - /usr/local/bin/vcfuniq [03:43:19] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:43:19] Found gzip - /bin/gzip [03:43:19] Found vt - /usr/local/bin/vt [03:43:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:43:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:43:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:43:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:43:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:43:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:43:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:43:20] Please supply a reference FASTA/GBK/EMBL file with --reference
1[03:43:22] This is snippy 4.6.0
Show full stderr[03:43:22] This is snippy 4.6.0 [03:43:22] Written by Torsten Seemann [03:43:22] Obtained from https://github.com/tseemann/snippy [03:43:22] Detected operating system: linux [03:43:22] Enabling bundled linux tools. [03:43:22] Found bwa - /usr/local/bin/bwa [03:43:22] Found bcftools - /usr/local/bin/bcftools [03:43:22] Found samtools - /usr/local/bin/samtools [03:43:22] Found java - /usr/local/bin/java [03:43:22] Found snpEff - /usr/local/bin/snpEff [03:43:22] Found samclip - /usr/local/bin/samclip [03:43:22] Found seqtk - /usr/local/bin/seqtk [03:43:22] Found parallel - /usr/local/bin/parallel [03:43:22] Found freebayes - /usr/local/bin/freebayes [03:43:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:43:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:43:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:43:22] Found vcfuniq - /usr/local/bin/vcfuniq [03:43:22] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:43:22] Found gzip - /bin/gzip [03:43:22] Found vt - /usr/local/bin/vt [03:43:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:43:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:43:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:43:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:43:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:43:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:43:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:43:23] Please supply a reference FASTA/GBK/EMBL file with --reference
1[03:43:34] This is snippy 4.6.0
Show full stderr[03:43:34] This is snippy 4.6.0 [03:43:34] Written by Torsten Seemann [03:43:34] Obtained from https://github.com/tseemann/snippy [03:43:34] Detected operating system: linux [03:43:34] Enabling bundled linux tools. [03:43:34] Found bwa - /usr/local/bin/bwa [03:43:34] Found bcftools - /usr/local/bin/bcftools [03:43:34] Found samtools - /usr/local/bin/samtools [03:43:34] Found java - /usr/local/bin/java [03:43:34] Found snpEff - /usr/local/bin/snpEff [03:43:34] Found samclip - /usr/local/bin/samclip [03:43:34] Found seqtk - /usr/local/bin/seqtk [03:43:34] Found parallel - /usr/local/bin/parallel [03:43:34] Found freebayes - /usr/local/bin/freebayes [03:43:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:43:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:43:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:43:34] Found vcfuniq - /usr/local/bin/vcfuniq [03:43:34] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:43:34] Found gzip - /bin/gzip [03:43:34] Found vt - /usr/local/bin/vt [03:43:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:43:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:43:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:43:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:43:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:43:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:43:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:43:35] Please supply a reference FASTA/GBK/EMBL file with --reference
1[03:43:44] This is snippy 4.6.0
Show full stderr[03:43:44] This is snippy 4.6.0 [03:43:44] Written by Torsten Seemann [03:43:44] Obtained from https://github.com/tseemann/snippy [03:43:44] Detected operating system: linux [03:43:44] Enabling bundled linux tools. [03:43:44] Found bwa - /usr/local/bin/bwa [03:43:44] Found bcftools - /usr/local/bin/bcftools [03:43:44] Found samtools - /usr/local/bin/samtools [03:43:44] Found java - /usr/local/bin/java [03:43:44] Found snpEff - /usr/local/bin/snpEff [03:43:44] Found samclip - /usr/local/bin/samclip [03:43:44] Found seqtk - /usr/local/bin/seqtk [03:43:44] Found parallel - /usr/local/bin/parallel [03:43:44] Found freebayes - /usr/local/bin/freebayes [03:43:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:43:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:43:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:43:44] Found vcfuniq - /usr/local/bin/vcfuniq [03:43:44] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:43:44] Found gzip - /bin/gzip [03:43:44] Found vt - /usr/local/bin/vt [03:43:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:43:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:43:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:43:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:43:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:43:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:43:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:43:45] Please supply a reference FASTA/GBK/EMBL file with --reference
1[03:42:18] This is snippy 4.6.0
Show full stderr[03:42:18] This is snippy 4.6.0 [03:42:18] Written by Torsten Seemann [03:42:18] Obtained from https://github.com/tseemann/snippy [03:42:18] Detected operating system: linux [03:42:18] Enabling bundled linux tools. [03:42:18] Found bwa - /usr/local/bin/bwa [03:42:18] Found bcftools - /usr/local/bin/bcftools [03:42:18] Found samtools - /usr/local/bin/samtools [03:42:18] Found java - /usr/local/bin/java [03:42:18] Found snpEff - /usr/local/bin/snpEff [03:42:18] Found samclip - /usr/local/bin/samclip [03:42:18] Found seqtk - /usr/local/bin/seqtk [03:42:18] Found parallel - /usr/local/bin/parallel [03:42:18] Found freebayes - /usr/local/bin/freebayes [03:42:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:42:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:42:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:42:18] Found vcfuniq - /usr/local/bin/vcfuniq [03:42:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:42:18] Found gzip - /bin/gzip [03:42:18] Found vt - /usr/local/bin/vt [03:42:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:42:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:42:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:42:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:42:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:42:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:42:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:42:19] Please supply a reference FASTA/GBK/EMBL file with --reference
1[03:42:22] This is snippy 4.6.0
Show full stderr[03:42:22] This is snippy 4.6.0 [03:42:22] Written by Torsten Seemann [03:42:22] Obtained from https://github.com/tseemann/snippy [03:42:22] Detected operating system: linux [03:42:22] Enabling bundled linux tools. [03:42:22] Found bwa - /usr/local/bin/bwa [03:42:22] Found bcftools - /usr/local/bin/bcftools [03:42:22] Found samtools - /usr/local/bin/samtools [03:42:22] Found java - /usr/local/bin/java [03:42:22] Found snpEff - /usr/local/bin/snpEff [03:42:22] Found samclip - /usr/local/bin/samclip [03:42:22] Found seqtk - /usr/local/bin/seqtk [03:42:22] Found parallel - /usr/local/bin/parallel [03:42:22] Found freebayes - /usr/local/bin/freebayes [03:42:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:42:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:42:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:42:22] Found vcfuniq - /usr/local/bin/vcfuniq [03:42:22] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:42:22] Found gzip - /bin/gzip [03:42:22] Found vt - /usr/local/bin/vt [03:42:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:42:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:42:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:42:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:42:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:42:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:42:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:42:23] Please supply a reference FASTA/GBK/EMBL file with --reference
1[03:43:31] This is snippy 4.6.0
Show full stderr[03:43:31] This is snippy 4.6.0 [03:43:31] Written by Torsten Seemann [03:43:31] Obtained from https://github.com/tseemann/snippy [03:43:31] Detected operating system: linux [03:43:31] Enabling bundled linux tools. [03:43:31] Found bwa - /usr/local/bin/bwa [03:43:31] Found bcftools - /usr/local/bin/bcftools [03:43:31] Found samtools - /usr/local/bin/samtools [03:43:31] Found java - /usr/local/bin/java [03:43:31] Found snpEff - /usr/local/bin/snpEff [03:43:31] Found samclip - /usr/local/bin/samclip [03:43:31] Found seqtk - /usr/local/bin/seqtk [03:43:31] Found parallel - /usr/local/bin/parallel [03:43:31] Found freebayes - /usr/local/bin/freebayes [03:43:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:43:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:43:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:43:31] Found vcfuniq - /usr/local/bin/vcfuniq [03:43:31] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:43:31] Found gzip - /bin/gzip [03:43:31] Found vt - /usr/local/bin/vt [03:43:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:43:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:43:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:43:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:43:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:43:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:43:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:43:32] Please supply a reference FASTA/GBK/EMBL file with --reference
1[03:43:40] This is snippy 4.6.0
Show full stderr[03:43:40] This is snippy 4.6.0 [03:43:40] Written by Torsten Seemann [03:43:40] Obtained from https://github.com/tseemann/snippy [03:43:40] Detected operating system: linux [03:43:40] Enabling bundled linux tools. [03:43:40] Found bwa - /usr/local/bin/bwa [03:43:40] Found bcftools - /usr/local/bin/bcftools [03:43:40] Found samtools - /usr/local/bin/samtools [03:43:40] Found java - /usr/local/bin/java [03:43:40] Found snpEff - /usr/local/bin/snpEff [03:43:40] Found samclip - /usr/local/bin/samclip [03:43:40] Found seqtk - /usr/local/bin/seqtk [03:43:40] Found parallel - /usr/local/bin/parallel [03:43:40] Found freebayes - /usr/local/bin/freebayes [03:43:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:43:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:43:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:43:40] Found vcfuniq - /usr/local/bin/vcfuniq [03:43:40] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:43:40] Found gzip - /bin/gzip [03:43:40] Found vt - /usr/local/bin/vt [03:43:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:43:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:43:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:43:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:43:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:43:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:43:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:43:41] Please supply a reference FASTA/GBK/EMBL file with --reference
1[03:44:00] This is snippy 4.6.0
Show full stderr[03:44:00] This is snippy 4.6.0 [03:44:00] Written by Torsten Seemann [03:44:00] Obtained from https://github.com/tseemann/snippy [03:44:00] Detected operating system: linux [03:44:00] Enabling bundled linux tools. [03:44:00] Found bwa - /usr/local/bin/bwa [03:44:00] Found bcftools - /usr/local/bin/bcftools [03:44:00] Found samtools - /usr/local/bin/samtools [03:44:00] Found java - /usr/local/bin/java [03:44:00] Found snpEff - /usr/local/bin/snpEff [03:44:00] Found samclip - /usr/local/bin/samclip [03:44:00] Found seqtk - /usr/local/bin/seqtk [03:44:00] Found parallel - /usr/local/bin/parallel [03:44:00] Found freebayes - /usr/local/bin/freebayes [03:44:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:44:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:44:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:44:00] Found vcfuniq - /usr/local/bin/vcfuniq [03:44:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:44:00] Found gzip - /bin/gzip [03:44:00] Found vt - /usr/local/bin/vt [03:44:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:44:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:44:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:44:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:44:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:44:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:44:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:44:01] Please supply a reference FASTA/GBK/EMBL file with --reference
1[03:44:04] This is snippy 4.6.0
Show full stderr[03:44:04] This is snippy 4.6.0 [03:44:04] Written by Torsten Seemann [03:44:04] Obtained from https://github.com/tseemann/snippy [03:44:04] Detected operating system: linux [03:44:04] Enabling bundled linux tools. [03:44:04] Found bwa - /usr/local/bin/bwa [03:44:04] Found bcftools - /usr/local/bin/bcftools [03:44:04] Found samtools - /usr/local/bin/samtools [03:44:04] Found java - /usr/local/bin/java [03:44:04] Found snpEff - /usr/local/bin/snpEff [03:44:04] Found samclip - /usr/local/bin/samclip [03:44:04] Found seqtk - /usr/local/bin/seqtk [03:44:04] Found parallel - /usr/local/bin/parallel [03:44:04] Found freebayes - /usr/local/bin/freebayes [03:44:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:44:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:44:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:44:04] Found vcfuniq - /usr/local/bin/vcfuniq [03:44:04] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:44:04] Found gzip - /bin/gzip [03:44:04] Found vt - /usr/local/bin/vt [03:44:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:44:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:44:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:44:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:44:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:44:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:44:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:44:05] Please supply a reference FASTA/GBK/EMBL file with --reference
1[03:44:20] This is snippy 4.6.0
Show full stderr[03:44:20] This is snippy 4.6.0 [03:44:20] Written by Torsten Seemann [03:44:20] Obtained from https://github.com/tseemann/snippy [03:44:20] Detected operating system: linux [03:44:20] Enabling bundled linux tools. [03:44:20] Found bwa - /usr/local/bin/bwa [03:44:20] Found bcftools - /usr/local/bin/bcftools [03:44:20] Found samtools - /usr/local/bin/samtools [03:44:20] Found java - /usr/local/bin/java [03:44:20] Found snpEff - /usr/local/bin/snpEff [03:44:20] Found samclip - /usr/local/bin/samclip [03:44:20] Found seqtk - /usr/local/bin/seqtk [03:44:20] Found parallel - /usr/local/bin/parallel [03:44:20] Found freebayes - /usr/local/bin/freebayes [03:44:20] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:44:20] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:44:20] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:44:20] Found vcfuniq - /usr/local/bin/vcfuniq [03:44:20] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:44:20] Found gzip - /bin/gzip [03:44:20] Found vt - /usr/local/bin/vt [03:44:20] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:44:20] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:44:20] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:44:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:44:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:44:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:44:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:44:21] Please supply a reference FASTA/GBK/EMBL file with --reference
1[03:42:13] This is snippy 4.6.0
Show full stderr[03:42:13] This is snippy 4.6.0 [03:42:13] Written by Torsten Seemann [03:42:13] Obtained from https://github.com/tseemann/snippy [03:42:13] Detected operating system: linux [03:42:13] Enabling bundled linux tools. [03:42:13] Found bwa - /usr/local/bin/bwa [03:42:13] Found bcftools - /usr/local/bin/bcftools [03:42:13] Found samtools - /usr/local/bin/samtools [03:42:13] Found java - /usr/local/bin/java [03:42:13] Found snpEff - /usr/local/bin/snpEff [03:42:13] Found samclip - /usr/local/bin/samclip [03:42:13] Found seqtk - /usr/local/bin/seqtk [03:42:13] Found parallel - /usr/local/bin/parallel [03:42:13] Found freebayes - /usr/local/bin/freebayes [03:42:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:42:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:42:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:42:13] Found vcfuniq - /usr/local/bin/vcfuniq [03:42:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:42:13] Found gzip - /bin/gzip [03:42:13] Found vt - /usr/local/bin/vt [03:42:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:42:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:42:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:42:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:42:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:42:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:42:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:42:15] Please supply a reference FASTA/GBK/EMBL file with --reference
1[03:42:50] This is snippy 4.6.0
Show full stderr[03:42:50] This is snippy 4.6.0 [03:42:50] Written by Torsten Seemann [03:42:50] Obtained from https://github.com/tseemann/snippy [03:42:50] Detected operating system: linux [03:42:50] Enabling bundled linux tools. [03:42:50] Found bwa - /usr/local/bin/bwa [03:42:50] Found bcftools - /usr/local/bin/bcftools [03:42:50] Found samtools - /usr/local/bin/samtools [03:42:50] Found java - /usr/local/bin/java [03:42:50] Found snpEff - /usr/local/bin/snpEff [03:42:50] Found samclip - /usr/local/bin/samclip [03:42:50] Found seqtk - /usr/local/bin/seqtk [03:42:50] Found parallel - /usr/local/bin/parallel [03:42:50] Found freebayes - /usr/local/bin/freebayes [03:42:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:42:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:42:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:42:50] Found vcfuniq - /usr/local/bin/vcfuniq [03:42:50] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:42:50] Found gzip - /bin/gzip [03:42:50] Found vt - /usr/local/bin/vt [03:42:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:42:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:42:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:42:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:42:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:42:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:42:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:42:52] Please supply a reference FASTA/GBK/EMBL file with --reference
1[03:43:14] This is snippy 4.6.0
Show full stderr[03:43:14] This is snippy 4.6.0 [03:43:14] Written by Torsten Seemann [03:43:14] Obtained from https://github.com/tseemann/snippy [03:43:14] Detected operating system: linux [03:43:14] Enabling bundled linux tools. [03:43:14] Found bwa - /usr/local/bin/bwa [03:43:14] Found bcftools - /usr/local/bin/bcftools [03:43:14] Found samtools - /usr/local/bin/samtools [03:43:14] Found java - /usr/local/bin/java [03:43:14] Found snpEff - /usr/local/bin/snpEff [03:43:14] Found samclip - /usr/local/bin/samclip [03:43:14] Found seqtk - /usr/local/bin/seqtk [03:43:14] Found parallel - /usr/local/bin/parallel [03:43:14] Found freebayes - /usr/local/bin/freebayes [03:43:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:43:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:43:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:43:14] Found vcfuniq - /usr/local/bin/vcfuniq [03:43:14] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:43:14] Found gzip - /bin/gzip [03:43:14] Found vt - /usr/local/bin/vt [03:43:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:43:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:43:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:43:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:43:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:43:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:43:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:43:15] Please supply a reference FASTA/GBK/EMBL file with --reference
1[03:43:25] This is snippy 4.6.0
Show full stderr[03:43:25] This is snippy 4.6.0 [03:43:25] Written by Torsten Seemann [03:43:25] Obtained from https://github.com/tseemann/snippy [03:43:25] Detected operating system: linux [03:43:25] Enabling bundled linux tools. [03:43:25] Found bwa - /usr/local/bin/bwa [03:43:25] Found bcftools - /usr/local/bin/bcftools [03:43:25] Found samtools - /usr/local/bin/samtools [03:43:25] Found java - /usr/local/bin/java [03:43:25] Found snpEff - /usr/local/bin/snpEff [03:43:25] Found samclip - /usr/local/bin/samclip [03:43:25] Found seqtk - /usr/local/bin/seqtk [03:43:25] Found parallel - /usr/local/bin/parallel [03:43:25] Found freebayes - /usr/local/bin/freebayes [03:43:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:43:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:43:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:43:25] Found vcfuniq - /usr/local/bin/vcfuniq [03:43:25] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:43:25] Found gzip - /bin/gzip [03:43:25] Found vt - /usr/local/bin/vt [03:43:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:43:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:43:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:43:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:43:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:43:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:43:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:43:26] Please supply a reference FASTA/GBK/EMBL file with --reference
1[03:43:37] This is snippy 4.6.0
Show full stderr[03:43:37] This is snippy 4.6.0 [03:43:37] Written by Torsten Seemann [03:43:37] Obtained from https://github.com/tseemann/snippy [03:43:37] Detected operating system: linux [03:43:37] Enabling bundled linux tools. [03:43:37] Found bwa - /usr/local/bin/bwa [03:43:37] Found bcftools - /usr/local/bin/bcftools [03:43:37] Found samtools - /usr/local/bin/samtools [03:43:37] Found java - /usr/local/bin/java [03:43:37] Found snpEff - /usr/local/bin/snpEff [03:43:37] Found samclip - /usr/local/bin/samclip [03:43:37] Found seqtk - /usr/local/bin/seqtk [03:43:37] Found parallel - /usr/local/bin/parallel [03:43:37] Found freebayes - /usr/local/bin/freebayes [03:43:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:43:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:43:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:43:37] Found vcfuniq - /usr/local/bin/vcfuniq [03:43:37] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:43:37] Found gzip - /bin/gzip [03:43:37] Found vt - /usr/local/bin/vt [03:43:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:43:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:43:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:43:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:43:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:43:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:43:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:43:38] Please supply a reference FASTA/GBK/EMBL file with --reference
1[03:43:49] This is snippy 4.6.0
Show full stderr[03:43:49] This is snippy 4.6.0 [03:43:49] Written by Torsten Seemann [03:43:49] Obtained from https://github.com/tseemann/snippy [03:43:49] Detected operating system: linux [03:43:49] Enabling bundled linux tools. [03:43:49] Found bwa - /usr/local/bin/bwa [03:43:49] Found bcftools - /usr/local/bin/bcftools [03:43:49] Found samtools - /usr/local/bin/samtools [03:43:49] Found java - /usr/local/bin/java [03:43:49] Found snpEff - /usr/local/bin/snpEff [03:43:49] Found samclip - /usr/local/bin/samclip [03:43:49] Found seqtk - /usr/local/bin/seqtk [03:43:49] Found parallel - /usr/local/bin/parallel [03:43:49] Found freebayes - /usr/local/bin/freebayes [03:43:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:43:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:43:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:43:49] Found vcfuniq - /usr/local/bin/vcfuniq [03:43:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:43:49] Found gzip - /bin/gzip [03:43:49] Found vt - /usr/local/bin/vt [03:43:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:43:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:43:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:43:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:43:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:43:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:43:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:43:50] Please supply a reference FASTA/GBK/EMBL file with --reference
1[03:43:52] This is snippy 4.6.0
Show full stderr[03:43:52] This is snippy 4.6.0 [03:43:52] Written by Torsten Seemann [03:43:52] Obtained from https://github.com/tseemann/snippy [03:43:52] Detected operating system: linux [03:43:52] Enabling bundled linux tools. [03:43:52] Found bwa - /usr/local/bin/bwa [03:43:52] Found bcftools - /usr/local/bin/bcftools [03:43:52] Found samtools - /usr/local/bin/samtools [03:43:52] Found java - /usr/local/bin/java [03:43:52] Found snpEff - /usr/local/bin/snpEff [03:43:52] Found samclip - /usr/local/bin/samclip [03:43:52] Found seqtk - /usr/local/bin/seqtk [03:43:52] Found parallel - /usr/local/bin/parallel [03:43:52] Found freebayes - /usr/local/bin/freebayes [03:43:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:43:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:43:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:43:52] Found vcfuniq - /usr/local/bin/vcfuniq [03:43:52] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:43:52] Found gzip - /bin/gzip [03:43:52] Found vt - /usr/local/bin/vt [03:43:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:43:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:43:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:43:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:43:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:43:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:43:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:43:53] Please supply a reference FASTA/GBK/EMBL file with --reference
1[03:44:10] This is snippy 4.6.0
Show full stderr[03:44:10] This is snippy 4.6.0 [03:44:10] Written by Torsten Seemann [03:44:10] Obtained from https://github.com/tseemann/snippy [03:44:10] Detected operating system: linux [03:44:10] Enabling bundled linux tools. [03:44:10] Found bwa - /usr/local/bin/bwa [03:44:10] Found bcftools - /usr/local/bin/bcftools [03:44:10] Found samtools - /usr/local/bin/samtools [03:44:10] Found java - /usr/local/bin/java [03:44:10] Found snpEff - /usr/local/bin/snpEff [03:44:10] Found samclip - /usr/local/bin/samclip [03:44:10] Found seqtk - /usr/local/bin/seqtk [03:44:10] Found parallel - /usr/local/bin/parallel [03:44:10] Found freebayes - /usr/local/bin/freebayes [03:44:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:44:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:44:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:44:10] Found vcfuniq - /usr/local/bin/vcfuniq [03:44:10] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:44:10] Found gzip - /bin/gzip [03:44:10] Found vt - /usr/local/bin/vt [03:44:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:44:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:44:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:44:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:44:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:44:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:44:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:44:11] Please supply a reference FASTA/GBK/EMBL file with --reference
1[03:43:07] This is snippy 4.6.0
Show full stderr[03:43:07] This is snippy 4.6.0 [03:43:07] Written by Torsten Seemann [03:43:07] Obtained from https://github.com/tseemann/snippy [03:43:07] Detected operating system: linux [03:43:07] Enabling bundled linux tools. [03:43:07] Found bwa - /usr/local/bin/bwa [03:43:07] Found bcftools - /usr/local/bin/bcftools [03:43:07] Found samtools - /usr/local/bin/samtools [03:43:07] Found java - /usr/local/bin/java [03:43:07] Found snpEff - /usr/local/bin/snpEff [03:43:07] Found samclip - /usr/local/bin/samclip [03:43:07] Found seqtk - /usr/local/bin/seqtk [03:43:07] Found parallel - /usr/local/bin/parallel [03:43:07] Found freebayes - /usr/local/bin/freebayes [03:43:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:43:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:43:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:43:07] Found vcfuniq - /usr/local/bin/vcfuniq [03:43:07] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:43:07] Found gzip - /bin/gzip [03:43:07] Found vt - /usr/local/bin/vt [03:43:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:43:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:43:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:43:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:43:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:43:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:43:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:43:08] Please supply a reference FASTA/GBK/EMBL file with --reference
1[03:43:55] This is snippy 4.6.0
Show full stderr[03:43:55] This is snippy 4.6.0 [03:43:55] Written by Torsten Seemann [03:43:55] Obtained from https://github.com/tseemann/snippy [03:43:55] Detected operating system: linux [03:43:55] Enabling bundled linux tools. [03:43:55] Found bwa - /usr/local/bin/bwa [03:43:55] Found bcftools - /usr/local/bin/bcftools [03:43:55] Found samtools - /usr/local/bin/samtools [03:43:55] Found java - /usr/local/bin/java [03:43:55] Found snpEff - /usr/local/bin/snpEff [03:43:55] Found samclip - /usr/local/bin/samclip [03:43:55] Found seqtk - /usr/local/bin/seqtk [03:43:55] Found parallel - /usr/local/bin/parallel [03:43:55] Found freebayes - /usr/local/bin/freebayes [03:43:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:43:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:43:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:43:55] Found vcfuniq - /usr/local/bin/vcfuniq [03:43:55] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:43:55] Found gzip - /bin/gzip [03:43:55] Found vt - /usr/local/bin/vt [03:43:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:43:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:43:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:43:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:43:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:43:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:43:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:43:56] Please supply a reference FASTA/GBK/EMBL file with --reference
1[03:44:07] This is snippy 4.6.0
Show full stderr[03:44:07] This is snippy 4.6.0 [03:44:07] Written by Torsten Seemann [03:44:07] Obtained from https://github.com/tseemann/snippy [03:44:07] Detected operating system: linux [03:44:07] Enabling bundled linux tools. [03:44:07] Found bwa - /usr/local/bin/bwa [03:44:07] Found bcftools - /usr/local/bin/bcftools [03:44:07] Found samtools - /usr/local/bin/samtools [03:44:07] Found java - /usr/local/bin/java [03:44:07] Found snpEff - /usr/local/bin/snpEff [03:44:07] Found samclip - /usr/local/bin/samclip [03:44:07] Found seqtk - /usr/local/bin/seqtk [03:44:07] Found parallel - /usr/local/bin/parallel [03:44:07] Found freebayes - /usr/local/bin/freebayes [03:44:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:44:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:44:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:44:07] Found vcfuniq - /usr/local/bin/vcfuniq [03:44:07] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:44:07] Found gzip - /bin/gzip [03:44:07] Found vt - /usr/local/bin/vt [03:44:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:44:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:44:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:44:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:44:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:44:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:44:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:44:08] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:57:26] This is snippy 4.6.0
Show full stderr[05:57:26] This is snippy 4.6.0 [05:57:26] Written by Torsten Seemann [05:57:26] Obtained from https://github.com/tseemann/snippy [05:57:26] Detected operating system: linux [05:57:26] Enabling bundled linux tools. [05:57:26] Found bwa - /usr/local/bin/bwa [05:57:26] Found bcftools - /usr/local/bin/bcftools [05:57:26] Found samtools - /usr/local/bin/samtools [05:57:26] Found java - /usr/local/bin/java [05:57:26] Found snpEff - /usr/local/bin/snpEff [05:57:26] Found samclip - /usr/local/bin/samclip [05:57:26] Found seqtk - /usr/local/bin/seqtk [05:57:26] Found parallel - /usr/local/bin/parallel [05:57:26] Found freebayes - /usr/local/bin/freebayes [05:57:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:57:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:57:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:57:26] Found vcfuniq - /usr/local/bin/vcfuniq [05:57:26] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:57:26] Found gzip - /bin/gzip [05:57:26] Found vt - /usr/local/bin/vt [05:57:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:57:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:57:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:57:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:57:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:57:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:57:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:57:27] Using reference: /cvmfs/data.galaxyproject.org/byhand/microbes/eschColi_APEC_O1/seq/eschColi_APEC_O1.fa [05:57:27] Treating reference as 'fasta' format. [05:57:27] Will use 1 CPU cores. [05:57:27] Using read file: /corral4/main/objects/0/7/a/dataset_07af536d-eb95-4af9-a0e8-c450eed562e8.dat [05:57:27] Creating folder: Resistance_27_fasta [05:57:27] Changing working directory: Resistance_27_fasta [05:57:27] Creating reference folder: reference [05:57:27] Extracting FASTA and GFF from reference. [05:57:28] Wrote 3 sequences to ref.fa [05:57:28] Wrote 0 features to ref.gff [05:57:28] Shredding /corral4/main/objects/0/7/a/dataset_07af536d-eb95-4af9-a0e8-c450eed562e8.dat into pseudo-reads [05:57:32] Wrote 468904 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [05:57:32] Freebayes will process 1 chunks of 5589314 bp, 1 chunks at a time. [05:57:32] Using BAM RG (Read Group) ID: Resistance_27_fasta [05:57:32] Running: samtools faidx reference/ref.fa 2>> snps.log [05:57:33] Running: bwa index reference/ref.fa 2>> snps.log [05:57:37] Error running command, check Resistance_27_fasta/snps.log
1[05:57:59] This is snippy 4.6.0
Show full stderr[05:57:59] This is snippy 4.6.0 [05:57:59] Written by Torsten Seemann [05:57:59] Obtained from https://github.com/tseemann/snippy [05:57:59] Detected operating system: linux [05:57:59] Enabling bundled linux tools. [05:57:59] Found bwa - /usr/local/bin/bwa [05:57:59] Found bcftools - /usr/local/bin/bcftools [05:57:59] Found samtools - /usr/local/bin/samtools [05:57:59] Found java - /usr/local/bin/java [05:57:59] Found snpEff - /usr/local/bin/snpEff [05:57:59] Found samclip - /usr/local/bin/samclip [05:57:59] Found seqtk - /usr/local/bin/seqtk [05:57:59] Found parallel - /usr/local/bin/parallel [05:57:59] Found freebayes - /usr/local/bin/freebayes [05:57:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:57:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:57:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:57:59] Found vcfuniq - /usr/local/bin/vcfuniq [05:57:59] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:57:59] Found gzip - /bin/gzip [05:57:59] Found vt - /usr/local/bin/vt [05:57:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:57:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:57:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:57:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:57:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:58:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:58:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:58:00] Using reference: /cvmfs/data.galaxyproject.org/byhand/microbes/eschColi_APEC_O1/seq/eschColi_APEC_O1.fa [05:58:00] Treating reference as 'fasta' format. [05:58:00] Will use 1 CPU cores. [05:58:00] Using read file: /corral4/main/objects/7/1/9/dataset_71939cda-582b-452b-8170-eff2e8633ec7.dat [05:58:00] Creating folder: Resistance_30_fasta [05:58:00] Changing working directory: Resistance_30_fasta [05:58:00] Creating reference folder: reference [05:58:00] Extracting FASTA and GFF from reference. [05:58:00] Wrote 3 sequences to ref.fa [05:58:00] Wrote 0 features to ref.gff [05:58:00] Shredding /corral4/main/objects/7/1/9/dataset_71939cda-582b-452b-8170-eff2e8633ec7.dat into pseudo-reads [05:58:04] Wrote 390940 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [05:58:05] Freebayes will process 1 chunks of 5589314 bp, 1 chunks at a time. [05:58:05] Using BAM RG (Read Group) ID: Resistance_30_fasta [05:58:05] Running: samtools faidx reference/ref.fa 2>> snps.log [05:58:05] Running: bwa index reference/ref.fa 2>> snps.log [05:58:08] Error running command, check Resistance_30_fasta/snps.log
1[05:58:28] This is snippy 4.6.0
Show full stderr[05:58:28] This is snippy 4.6.0 [05:58:28] Written by Torsten Seemann [05:58:28] Obtained from https://github.com/tseemann/snippy [05:58:28] Detected operating system: linux [05:58:28] Enabling bundled linux tools. [05:58:28] Found bwa - /usr/local/bin/bwa [05:58:28] Found bcftools - /usr/local/bin/bcftools [05:58:28] Found samtools - /usr/local/bin/samtools [05:58:28] Found java - /usr/local/bin/java [05:58:28] Found snpEff - /usr/local/bin/snpEff [05:58:28] Found samclip - /usr/local/bin/samclip [05:58:28] Found seqtk - /usr/local/bin/seqtk [05:58:28] Found parallel - /usr/local/bin/parallel [05:58:28] Found freebayes - /usr/local/bin/freebayes [05:58:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:58:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:58:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:58:28] Found vcfuniq - /usr/local/bin/vcfuniq [05:58:28] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:58:28] Found gzip - /bin/gzip [05:58:28] Found vt - /usr/local/bin/vt [05:58:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:58:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:58:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:58:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:58:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:58:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:58:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:58:29] Using reference: /cvmfs/data.galaxyproject.org/byhand/microbes/eschColi_APEC_O1/seq/eschColi_APEC_O1.fa [05:58:29] Treating reference as 'fasta' format. [05:58:29] Will use 1 CPU cores. [05:58:29] Using read file: /corral4/main/objects/d/f/0/dataset_df046bb5-b8f5-4480-a184-7f83a1019f83.dat [05:58:29] Creating folder: Resistance_68_fasta [05:58:29] Changing working directory: Resistance_68_fasta [05:58:29] Creating reference folder: reference [05:58:29] Extracting FASTA and GFF from reference. [05:58:29] Wrote 3 sequences to ref.fa [05:58:29] Wrote 0 features to ref.gff [05:58:29] Shredding /corral4/main/objects/d/f/0/dataset_df046bb5-b8f5-4480-a184-7f83a1019f83.dat into pseudo-reads [05:58:34] Wrote 438110 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [05:58:34] Freebayes will process 1 chunks of 5589314 bp, 1 chunks at a time. [05:58:34] Using BAM RG (Read Group) ID: Resistance_68_fasta [05:58:34] Running: samtools faidx reference/ref.fa 2>> snps.log [05:58:34] Running: bwa index reference/ref.fa 2>> snps.log [05:58:37] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [05:58:38] Running: ln -sf reference/ref.fa . 2>> snps.log [05:58:38] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [05:58:38] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [05:58:38] Running: bwa mem -Y -M -R '@RG\tID:Resistance_68_fasta\tSM:Resistance_68_fasta' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/258/72258621/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/258/72258621/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/258/72258621/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 3 sequences in reference/ref.fa.fai
1[05:58:32] This is snippy 4.6.0
Show full stderr[05:58:32] This is snippy 4.6.0 [05:58:32] Written by Torsten Seemann [05:58:32] Obtained from https://github.com/tseemann/snippy [05:58:32] Detected operating system: linux [05:58:32] Enabling bundled linux tools. [05:58:32] Found bwa - /usr/local/bin/bwa [05:58:32] Found bcftools - /usr/local/bin/bcftools [05:58:32] Found samtools - /usr/local/bin/samtools [05:58:32] Found java - /usr/local/bin/java [05:58:32] Found snpEff - /usr/local/bin/snpEff [05:58:32] Found samclip - /usr/local/bin/samclip [05:58:32] Found seqtk - /usr/local/bin/seqtk [05:58:32] Found parallel - /usr/local/bin/parallel [05:58:32] Found freebayes - /usr/local/bin/freebayes [05:58:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:58:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:58:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:58:32] Found vcfuniq - /usr/local/bin/vcfuniq [05:58:32] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:58:32] Found gzip - /bin/gzip [05:58:32] Found vt - /usr/local/bin/vt [05:58:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:58:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:58:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:58:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:58:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:58:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:58:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:58:33] Using reference: /cvmfs/data.galaxyproject.org/byhand/microbes/eschColi_APEC_O1/seq/eschColi_APEC_O1.fa [05:58:33] Treating reference as 'fasta' format. [05:58:33] Will use 1 CPU cores. [05:58:33] Using read file: /corral4/main/objects/4/b/f/dataset_4bf577f2-77f5-4d64-ad5f-a01e9e27fa4b.dat [05:58:33] Creating folder: Resistance_69_fasta [05:58:33] Changing working directory: Resistance_69_fasta [05:58:33] Creating reference folder: reference [05:58:33] Extracting FASTA and GFF from reference. [05:58:34] Wrote 3 sequences to ref.fa [05:58:34] Wrote 0 features to ref.gff [05:58:34] Shredding /corral4/main/objects/4/b/f/dataset_4bf577f2-77f5-4d64-ad5f-a01e9e27fa4b.dat into pseudo-reads [05:58:40] Wrote 400510 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [05:58:40] Freebayes will process 1 chunks of 5589314 bp, 1 chunks at a time. [05:58:40] Using BAM RG (Read Group) ID: Resistance_69_fasta [05:58:40] Running: samtools faidx reference/ref.fa 2>> snps.log [05:58:40] Running: bwa index reference/ref.fa 2>> snps.log [05:58:40] Error running command, check Resistance_69_fasta/snps.log
1[05:59:00] This is snippy 4.6.0
Show full stderr[05:59:00] This is snippy 4.6.0 [05:59:00] Written by Torsten Seemann [05:59:00] Obtained from https://github.com/tseemann/snippy [05:59:00] Detected operating system: linux [05:59:00] Enabling bundled linux tools. [05:59:00] Found bwa - /usr/local/bin/bwa [05:59:00] Found bcftools - /usr/local/bin/bcftools [05:59:00] Found samtools - /usr/local/bin/samtools [05:59:00] Found java - /usr/local/bin/java [05:59:00] Found snpEff - /usr/local/bin/snpEff [05:59:00] Found samclip - /usr/local/bin/samclip [05:59:00] Found seqtk - /usr/local/bin/seqtk [05:59:00] Found parallel - /usr/local/bin/parallel [05:59:00] Found freebayes - /usr/local/bin/freebayes [05:59:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:59:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:59:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:59:00] Found vcfuniq - /usr/local/bin/vcfuniq [05:59:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:59:00] Found gzip - /bin/gzip [05:59:00] Found vt - /usr/local/bin/vt [05:59:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:59:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:59:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:59:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:59:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:59:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:59:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:59:01] Using reference: /cvmfs/data.galaxyproject.org/byhand/microbes/eschColi_APEC_O1/seq/eschColi_APEC_O1.fa [05:59:01] Treating reference as 'fasta' format. [05:59:01] Will use 1 CPU cores. [05:59:01] Using read file: /corral4/main/objects/7/6/a/dataset_76aadc4d-ac2f-4192-8791-0fe4093b4122.dat [05:59:01] Creating folder: Resistance_73_fasta [05:59:01] Changing working directory: Resistance_73_fasta [05:59:01] Creating reference folder: reference [05:59:01] Extracting FASTA and GFF from reference. [05:59:01] Wrote 3 sequences to ref.fa [05:59:01] Wrote 0 features to ref.gff [05:59:01] Shredding /corral4/main/objects/7/6/a/dataset_76aadc4d-ac2f-4192-8791-0fe4093b4122.dat into pseudo-reads [05:59:06] Wrote 415842 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [05:59:06] Freebayes will process 1 chunks of 5589314 bp, 1 chunks at a time. [05:59:06] Using BAM RG (Read Group) ID: Resistance_73_fasta [05:59:07] Running: samtools faidx reference/ref.fa 2>> snps.log [05:59:07] Running: bwa index reference/ref.fa 2>> snps.log [05:59:11] Error running command, check Resistance_73_fasta/snps.log
1[05:53:24] This is snippy 4.6.0
Show full stderr[05:53:24] This is snippy 4.6.0 [05:53:24] Written by Torsten Seemann [05:53:24] Obtained from https://github.com/tseemann/snippy [05:53:24] Detected operating system: linux [05:53:24] Enabling bundled linux tools. [05:53:24] Found bwa - /usr/local/bin/bwa [05:53:24] Found bcftools - /usr/local/bin/bcftools [05:53:24] Found samtools - /usr/local/bin/samtools [05:53:24] Found java - /usr/local/bin/java [05:53:24] Found snpEff - /usr/local/bin/snpEff [05:53:24] Found samclip - /usr/local/bin/samclip [05:53:24] Found seqtk - /usr/local/bin/seqtk [05:53:24] Found parallel - /usr/local/bin/parallel [05:53:24] Found freebayes - /usr/local/bin/freebayes [05:53:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:53:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:53:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:53:24] Found vcfuniq - /usr/local/bin/vcfuniq [05:53:24] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:53:24] Found gzip - /bin/gzip [05:53:24] Found vt - /usr/local/bin/vt [05:53:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:53:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:53:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:53:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:53:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:53:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:53:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:53:26] Using reference: /cvmfs/data.galaxyproject.org/byhand/microbes/eschColi_APEC_O1/seq/eschColi_APEC_O1.fa [05:53:26] Treating reference as 'fasta' format. [05:53:26] Will use 1 CPU cores. [05:53:26] Using read file: /corral4/main/objects/4/4/7/dataset_447a024f-c0d7-46ab-a966-b2633c78f043.dat [05:53:26] Creating folder: Resistance_86_fasta [05:53:26] Changing working directory: Resistance_86_fasta [05:53:26] Creating reference folder: reference [05:53:26] Extracting FASTA and GFF from reference. [05:53:26] Wrote 3 sequences to ref.fa [05:53:26] Wrote 0 features to ref.gff [05:53:26] Shredding /corral4/main/objects/4/4/7/dataset_447a024f-c0d7-46ab-a966-b2633c78f043.dat into pseudo-reads [05:53:32] Wrote 422132 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [05:53:32] Freebayes will process 1 chunks of 5589314 bp, 1 chunks at a time. [05:53:32] Using BAM RG (Read Group) ID: Resistance_86_fasta [05:53:32] Running: samtools faidx reference/ref.fa 2>> snps.log [05:53:32] Running: bwa index reference/ref.fa 2>> snps.log [05:53:38] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [05:53:38] Running: ln -sf reference/ref.fa . 2>> snps.log [05:53:38] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [05:53:38] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [05:53:38] Running: bwa mem -Y -M -R '@RG\tID:Resistance_86_fasta\tSM:Resistance_86_fasta' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/258/72258639/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/258/72258639/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/258/72258639/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 3 sequences in reference/ref.fa.fai
1[05:54:28] This is snippy 4.6.0
Show full stderr[05:54:28] This is snippy 4.6.0 [05:54:28] Written by Torsten Seemann [05:54:28] Obtained from https://github.com/tseemann/snippy [05:54:28] Detected operating system: linux [05:54:28] Enabling bundled linux tools. [05:54:28] Found bwa - /usr/local/bin/bwa [05:54:28] Found bcftools - /usr/local/bin/bcftools [05:54:28] Found samtools - /usr/local/bin/samtools [05:54:28] Found java - /usr/local/bin/java [05:54:28] Found snpEff - /usr/local/bin/snpEff [05:54:28] Found samclip - /usr/local/bin/samclip [05:54:28] Found seqtk - /usr/local/bin/seqtk [05:54:28] Found parallel - /usr/local/bin/parallel [05:54:28] Found freebayes - /usr/local/bin/freebayes [05:54:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:54:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:54:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:54:28] Found vcfuniq - /usr/local/bin/vcfuniq [05:54:28] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:54:28] Found gzip - /bin/gzip [05:54:28] Found vt - /usr/local/bin/vt [05:54:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:54:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:54:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:54:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:54:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:54:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:54:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:54:29] Using reference: /cvmfs/data.galaxyproject.org/byhand/microbes/eschColi_APEC_O1/seq/eschColi_APEC_O1.fa [05:54:29] Treating reference as 'fasta' format. [05:54:29] Will use 1 CPU cores. [05:54:29] Using read file: /corral4/main/objects/8/2/5/dataset_82599e38-094b-42ab-b0d7-d5e591dc0b91.dat [05:54:29] Creating folder: Resistance_87_fasta [05:54:29] Changing working directory: Resistance_87_fasta [05:54:29] Creating reference folder: reference [05:54:29] Extracting FASTA and GFF from reference. [05:54:29] Wrote 3 sequences to ref.fa [05:54:29] Wrote 0 features to ref.gff [05:54:29] Shredding /corral4/main/objects/8/2/5/dataset_82599e38-094b-42ab-b0d7-d5e591dc0b91.dat into pseudo-reads [05:54:34] Wrote 423030 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [05:54:34] Freebayes will process 1 chunks of 5589314 bp, 1 chunks at a time. [05:54:34] Using BAM RG (Read Group) ID: Resistance_87_fasta [05:54:34] Running: samtools faidx reference/ref.fa 2>> snps.log [05:54:34] Running: bwa index reference/ref.fa 2>> snps.log [05:54:37] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [05:54:37] Running: ln -sf reference/ref.fa . 2>> snps.log [05:54:37] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [05:54:37] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [05:54:37] Running: bwa mem -Y -M -R '@RG\tID:Resistance_87_fasta\tSM:Resistance_87_fasta' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/258/72258640/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/258/72258640/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/258/72258640/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 3 sequences in reference/ref.fa.fai
1[05:55:59] This is snippy 4.6.0
Show full stderr[05:55:59] This is snippy 4.6.0 [05:55:59] Written by Torsten Seemann [05:55:59] Obtained from https://github.com/tseemann/snippy [05:55:59] Detected operating system: linux [05:55:59] Enabling bundled linux tools. [05:55:59] Found bwa - /usr/local/bin/bwa [05:55:59] Found bcftools - /usr/local/bin/bcftools [05:55:59] Found samtools - /usr/local/bin/samtools [05:55:59] Found java - /usr/local/bin/java [05:55:59] Found snpEff - /usr/local/bin/snpEff [05:55:59] Found samclip - /usr/local/bin/samclip [05:55:59] Found seqtk - /usr/local/bin/seqtk [05:55:59] Found parallel - /usr/local/bin/parallel [05:55:59] Found freebayes - /usr/local/bin/freebayes [05:55:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:55:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:55:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:55:59] Found vcfuniq - /usr/local/bin/vcfuniq [05:55:59] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:56:00] Found gzip - /bin/gzip [05:56:00] Found vt - /usr/local/bin/vt [05:56:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:56:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:56:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:56:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:56:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:56:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:56:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:56:01] Using reference: /cvmfs/data.galaxyproject.org/byhand/microbes/eschColi_APEC_O1/seq/eschColi_APEC_O1.fa [05:56:01] Treating reference as 'fasta' format. [05:56:01] Will use 1 CPU cores. [05:56:01] Using read file: /corral4/main/objects/1/b/7/dataset_1b7cfb67-2d85-4140-9a62-51a430d8aa97.dat [05:56:01] Creating folder: Resistance_89_fasta [05:56:01] Changing working directory: Resistance_89_fasta [05:56:01] Creating reference folder: reference [05:56:01] Extracting FASTA and GFF from reference. [05:56:01] Wrote 3 sequences to ref.fa [05:56:01] Wrote 0 features to ref.gff [05:56:01] Shredding /corral4/main/objects/1/b/7/dataset_1b7cfb67-2d85-4140-9a62-51a430d8aa97.dat into pseudo-reads [05:56:06] Wrote 411052 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [05:56:06] Freebayes will process 1 chunks of 5589314 bp, 1 chunks at a time. [05:56:06] Using BAM RG (Read Group) ID: Resistance_89_fasta [05:56:06] Running: samtools faidx reference/ref.fa 2>> snps.log [05:56:06] Running: bwa index reference/ref.fa 2>> snps.log [05:56:11] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [05:56:11] Running: ln -sf reference/ref.fa . 2>> snps.log [05:56:11] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [05:56:11] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [05:56:11] Running: bwa mem -Y -M -R '@RG\tID:Resistance_89_fasta\tSM:Resistance_89_fasta' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/258/72258641/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/258/72258641/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/258/72258641/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 3 sequences in reference/ref.fa.fai
1[05:57:12] This is snippy 4.6.0
Show full stderr[05:57:12] This is snippy 4.6.0 [05:57:12] Written by Torsten Seemann [05:57:12] Obtained from https://github.com/tseemann/snippy [05:57:12] Detected operating system: linux [05:57:12] Enabling bundled linux tools. [05:57:12] Found bwa - /usr/local/bin/bwa [05:57:12] Found bcftools - /usr/local/bin/bcftools [05:57:12] Found samtools - /usr/local/bin/samtools [05:57:12] Found java - /usr/local/bin/java [05:57:12] Found snpEff - /usr/local/bin/snpEff [05:57:12] Found samclip - /usr/local/bin/samclip [05:57:12] Found seqtk - /usr/local/bin/seqtk [05:57:12] Found parallel - /usr/local/bin/parallel [05:57:12] Found freebayes - /usr/local/bin/freebayes [05:57:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:57:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:57:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:57:12] Found vcfuniq - /usr/local/bin/vcfuniq [05:57:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:57:12] Found gzip - /bin/gzip [05:57:12] Found vt - /usr/local/bin/vt [05:57:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:57:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:57:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:57:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:57:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:57:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:57:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:57:14] Using reference: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat [05:57:14] Treating reference as 'fasta' format. [05:57:14] Will use 1 CPU cores. [05:57:14] Using read file: /corral4/main/objects/b/4/b/dataset_b4b28949-0cba-496c-9eba-8bb6e332013e.dat [05:57:14] Creating folder: GCF_005144725_1_ASM514472v1_genomic_fna [05:57:14] Changing working directory: GCF_005144725_1_ASM514472v1_genomic_fna [05:57:14] Creating reference folder: reference [05:57:14] Extracting FASTA and GFF from reference. [05:57:15] Wrote 1 sequences to ref.fa [05:57:15] Wrote 0 features to ref.gff [05:57:15] Shredding /corral4/main/objects/b/4/b/dataset_b4b28949-0cba-496c-9eba-8bb6e332013e.dat into pseudo-reads [05:57:18] Wrote 355626 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [05:57:18] Freebayes will process 1 chunks of 4485121 bp, 1 chunks at a time. [05:57:18] Using BAM RG (Read Group) ID: GCF_005144725_1_ASM514472v1_genomic_fna [05:57:18] Running: samtools faidx reference/ref.fa 2>> snps.log [05:57:19] Running: bwa index reference/ref.fa 2>> snps.log [05:57:24] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [05:57:24] Running: ln -sf reference/ref.fa . 2>> snps.log [05:57:24] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [05:57:24] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [05:57:24] Running: bwa mem -Y -M -R '@RG\tID:GCF_005144725_1_ASM514472v1_genomic_fna\tSM:GCF_005144725_1_ASM514472v1_genomic_fna' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/260/72260487/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/260/72260487/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/260/72260487/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip]
1[05:56:35] This is snippy 4.6.0
Show full stderr[05:56:35] This is snippy 4.6.0 [05:56:35] Written by Torsten Seemann [05:56:35] Obtained from https://github.com/tseemann/snippy [05:56:35] Detected operating system: linux [05:56:35] Enabling bundled linux tools. [05:56:35] Found bwa - /usr/local/bin/bwa [05:56:35] Found bcftools - /usr/local/bin/bcftools [05:56:35] Found samtools - /usr/local/bin/samtools [05:56:35] Found java - /usr/local/bin/java [05:56:35] Found snpEff - /usr/local/bin/snpEff [05:56:35] Found samclip - /usr/local/bin/samclip [05:56:35] Found seqtk - /usr/local/bin/seqtk [05:56:35] Found parallel - /usr/local/bin/parallel [05:56:35] Found freebayes - /usr/local/bin/freebayes [05:56:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:56:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:56:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:56:35] Found vcfuniq - /usr/local/bin/vcfuniq [05:56:35] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:56:35] Found gzip - /bin/gzip [05:56:35] Found vt - /usr/local/bin/vt [05:56:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:56:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:56:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:56:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:56:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:56:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:56:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:56:36] Using reference: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat [05:56:36] Treating reference as 'fasta' format. [05:56:36] Will use 1 CPU cores. [05:56:36] Using read file: /corral4/main/objects/4/c/6/dataset_4c6552aa-c652-4a08-9a51-7d0c28a4126a.dat [05:56:36] Creating folder: GCA_019661335_1_ASM1966133v1_genomic_fna [05:56:36] Changing working directory: GCA_019661335_1_ASM1966133v1_genomic_fna [05:56:36] Creating reference folder: reference [05:56:36] Extracting FASTA and GFF from reference. [05:56:36] Wrote 1 sequences to ref.fa [05:56:36] Wrote 0 features to ref.gff [05:56:36] Shredding /corral4/main/objects/4/c/6/dataset_4c6552aa-c652-4a08-9a51-7d0c28a4126a.dat into pseudo-reads [05:56:40] Wrote 436000 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [05:56:40] Freebayes will process 1 chunks of 4485121 bp, 1 chunks at a time. [05:56:40] Using BAM RG (Read Group) ID: GCA_019661335_1_ASM1966133v1_genomic_fna [05:56:40] Running: samtools faidx reference/ref.fa 2>> snps.log [05:56:40] Running: bwa index reference/ref.fa 2>> snps.log [05:56:42] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [05:56:42] Running: ln -sf reference/ref.fa . 2>> snps.log [05:56:42] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [05:56:42] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [05:56:42] Running: bwa mem -Y -M -R '@RG\tID:GCA_019661335_1_ASM1966133v1_genomic_fna\tSM:GCA_019661335_1_ASM1966133v1_genomic_fna' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/260/72260519/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/260/72260519/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/260/72260519/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [sam
1[05:58:10] This is snippy 4.6.0
Show full stderr[05:58:10] This is snippy 4.6.0 [05:58:10] Written by Torsten Seemann [05:58:10] Obtained from https://github.com/tseemann/snippy [05:58:10] Detected operating system: linux [05:58:10] Enabling bundled linux tools. [05:58:10] Found bwa - /usr/local/bin/bwa [05:58:10] Found bcftools - /usr/local/bin/bcftools [05:58:10] Found samtools - /usr/local/bin/samtools [05:58:10] Found java - /usr/local/bin/java [05:58:10] Found snpEff - /usr/local/bin/snpEff [05:58:10] Found samclip - /usr/local/bin/samclip [05:58:10] Found seqtk - /usr/local/bin/seqtk [05:58:10] Found parallel - /usr/local/bin/parallel [05:58:10] Found freebayes - /usr/local/bin/freebayes [05:58:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:58:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:58:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:58:10] Found vcfuniq - /usr/local/bin/vcfuniq [05:58:10] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:58:10] Found gzip - /bin/gzip [05:58:10] Found vt - /usr/local/bin/vt [05:58:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:58:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:58:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:58:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:58:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:58:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:58:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:58:11] Using reference: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat [05:58:11] Treating reference as 'fasta' format. [05:58:11] Will use 1 CPU cores. [05:58:11] Using read file: /corral4/main/objects/3/9/4/dataset_3947c198-e6d1-4c51-8840-17091505addc.dat [05:58:11] Creating folder: GCA_019661385_1_ASM1966138v1_genomic_fna [05:58:11] Changing working directory: GCA_019661385_1_ASM1966138v1_genomic_fna [05:58:11] Creating reference folder: reference [05:58:11] Extracting FASTA and GFF from reference. [05:58:11] Wrote 1 sequences to ref.fa [05:58:11] Wrote 0 features to ref.gff [05:58:11] Shredding /corral4/main/objects/3/9/4/dataset_3947c198-e6d1-4c51-8840-17091505addc.dat into pseudo-reads [05:58:16] Wrote 447600 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [05:58:16] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time. [05:58:16] Using BAM RG (Read Group) ID: GCA_019661385_1_ASM1966138v1_genomic_fna [05:58:16] Running: samtools faidx reference/ref.fa 2>> snps.log [05:58:16] Error running command, check GCA_019661385_1_ASM1966138v1_genomic_fna/snps.log
1[05:59:38] This is snippy 4.6.0
Show full stderr[05:59:38] This is snippy 4.6.0 [05:59:38] Written by Torsten Seemann [05:59:38] Obtained from https://github.com/tseemann/snippy [05:59:38] Detected operating system: linux [05:59:38] Enabling bundled linux tools. [05:59:38] Found bwa - /usr/local/bin/bwa [05:59:38] Found bcftools - /usr/local/bin/bcftools [05:59:38] Found samtools - /usr/local/bin/samtools [05:59:38] Found java - /usr/local/bin/java [05:59:38] Found snpEff - /usr/local/bin/snpEff [05:59:38] Found samclip - /usr/local/bin/samclip [05:59:38] Found seqtk - /usr/local/bin/seqtk [05:59:38] Found parallel - /usr/local/bin/parallel [05:59:38] Found freebayes - /usr/local/bin/freebayes [05:59:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:59:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:59:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:59:38] Found vcfuniq - /usr/local/bin/vcfuniq [05:59:38] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:59:38] Found gzip - /bin/gzip [05:59:38] Found vt - /usr/local/bin/vt [05:59:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:59:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:59:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:59:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:59:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:59:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:59:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:59:39] Using reference: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat [05:59:39] Treating reference as 'fasta' format. [05:59:39] Will use 1 CPU cores. [05:59:39] Using read file: /corral4/main/objects/5/0/e/dataset_50ebb9d0-52f7-47f9-b652-9c2be03cc94c.dat [05:59:39] Creating folder: GCF_002447215_1_ASM244721v1_genomic_fna [05:59:39] Changing working directory: GCF_002447215_1_ASM244721v1_genomic_fna [05:59:39] Creating reference folder: reference [05:59:39] Extracting FASTA and GFF from reference. [05:59:39] Wrote 1 sequences to ref.fa [05:59:39] Wrote 0 features to ref.gff [05:59:39] Shredding /corral4/main/objects/5/0/e/dataset_50ebb9d0-52f7-47f9-b652-9c2be03cc94c.dat into pseudo-reads [05:59:43] Wrote 352948 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [05:59:43] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time. [05:59:43] Using BAM RG (Read Group) ID: GCF_002447215_1_ASM244721v1_genomic_fna [05:59:43] Running: samtools faidx reference/ref.fa 2>> snps.log [05:59:43] Error running command, check GCF_002447215_1_ASM244721v1_genomic_fna/snps.log
1[05:55:53] This is snippy 4.6.0
Show full stderr[05:55:53] This is snippy 4.6.0 [05:55:53] Written by Torsten Seemann [05:55:53] Obtained from https://github.com/tseemann/snippy [05:55:53] Detected operating system: linux [05:55:53] Enabling bundled linux tools. [05:55:53] Found bwa - /usr/local/bin/bwa [05:55:53] Found bcftools - /usr/local/bin/bcftools [05:55:53] Found samtools - /usr/local/bin/samtools [05:55:53] Found java - /usr/local/bin/java [05:55:53] Found snpEff - /usr/local/bin/snpEff [05:55:53] Found samclip - /usr/local/bin/samclip [05:55:53] Found seqtk - /usr/local/bin/seqtk [05:55:53] Found parallel - /usr/local/bin/parallel [05:55:53] Found freebayes - /usr/local/bin/freebayes [05:55:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:55:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:55:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:55:53] Found vcfuniq - /usr/local/bin/vcfuniq [05:55:53] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:55:53] Found gzip - /bin/gzip [05:55:53] Found vt - /usr/local/bin/vt [05:55:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:55:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:55:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:55:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:55:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:55:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:55:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:55:55] Using reference: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat [05:55:55] Treating reference as 'fasta' format. [05:55:55] Will use 1 CPU cores. [05:55:55] Using read file: /corral4/main/objects/7/6/a/dataset_76a18bff-8cf6-43ba-94b7-fbb3d96ef5fa.dat [05:55:55] Creating folder: GCF_003006135_1_ASM300613v1_genomic_fna [05:55:55] Changing working directory: GCF_003006135_1_ASM300613v1_genomic_fna [05:55:55] Creating reference folder: reference [05:55:55] Extracting FASTA and GFF from reference. [05:55:55] Wrote 1 sequences to ref.fa [05:55:55] Wrote 0 features to ref.gff [05:55:55] Shredding /corral4/main/objects/7/6/a/dataset_76a18bff-8cf6-43ba-94b7-fbb3d96ef5fa.dat into pseudo-reads [05:55:59] Wrote 353138 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [05:55:59] Freebayes will process 1 chunks of 4485121 bp, 1 chunks at a time. [05:55:59] Using BAM RG (Read Group) ID: GCF_003006135_1_ASM300613v1_genomic_fna [05:55:59] Running: samtools faidx reference/ref.fa 2>> snps.log [05:55:59] Running: bwa index reference/ref.fa 2>> snps.log [05:56:04] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [05:56:04] Running: ln -sf reference/ref.fa . 2>> snps.log [05:56:04] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [05:56:04] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [05:56:04] Running: bwa mem -Y -M -R '@RG\tID:GCF_003006135_1_ASM300613v1_genomic_fna\tSM:GCF_003006135_1_ASM300613v1_genomic_fna' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/260/72260549/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/260/72260549/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/260/72260549/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip]
1[05:57:53] This is snippy 4.6.0
Show full stderr[05:57:53] This is snippy 4.6.0 [05:57:53] Written by Torsten Seemann [05:57:53] Obtained from https://github.com/tseemann/snippy [05:57:53] Detected operating system: linux [05:57:53] Enabling bundled linux tools. [05:57:53] Found bwa - /usr/local/bin/bwa [05:57:53] Found bcftools - /usr/local/bin/bcftools [05:57:53] Found samtools - /usr/local/bin/samtools [05:57:53] Found java - /usr/local/bin/java [05:57:53] Found snpEff - /usr/local/bin/snpEff [05:57:53] Found samclip - /usr/local/bin/samclip [05:57:53] Found seqtk - /usr/local/bin/seqtk [05:57:53] Found parallel - /usr/local/bin/parallel [05:57:53] Found freebayes - /usr/local/bin/freebayes [05:57:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:57:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:57:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:57:53] Found vcfuniq - /usr/local/bin/vcfuniq [05:57:53] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:57:53] Found gzip - /bin/gzip [05:57:53] Found vt - /usr/local/bin/vt [05:57:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:57:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:57:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:57:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:57:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:57:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:57:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:57:54] Using reference: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat [05:57:54] Treating reference as 'fasta' format. [05:57:54] Will use 1 CPU cores. [05:57:54] Using read file: /corral4/main/objects/0/5/e/dataset_05e984c9-f75e-41a8-add8-d623160bf91e.dat [05:57:54] Creating folder: GCF_002591875_1_ASM259187v1_genomic_fna [05:57:54] Changing working directory: GCF_002591875_1_ASM259187v1_genomic_fna [05:57:54] Creating reference folder: reference [05:57:54] Extracting FASTA and GFF from reference. [05:57:54] Wrote 1 sequences to ref.fa [05:57:54] Wrote 0 features to ref.gff [05:57:54] Shredding /corral4/main/objects/0/5/e/dataset_05e984c9-f75e-41a8-add8-d623160bf91e.dat into pseudo-reads [05:57:58] Wrote 351844 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [05:57:58] Freebayes will process 1 chunks of 4485121 bp, 1 chunks at a time. [05:57:58] Using BAM RG (Read Group) ID: GCF_002591875_1_ASM259187v1_genomic_fna [05:57:58] Running: samtools faidx reference/ref.fa 2>> snps.log [05:57:58] Running: bwa index reference/ref.fa 2>> snps.log [05:58:01] Error running command, check GCF_002591875_1_ASM259187v1_genomic_fna/snps.log
1[05:56:15] This is snippy 4.6.0
Show full stderr[05:56:15] This is snippy 4.6.0 [05:56:15] Written by Torsten Seemann [05:56:15] Obtained from https://github.com/tseemann/snippy [05:56:15] Detected operating system: linux [05:56:15] Enabling bundled linux tools. [05:56:15] Found bwa - /usr/local/bin/bwa [05:56:15] Found bcftools - /usr/local/bin/bcftools [05:56:15] Found samtools - /usr/local/bin/samtools [05:56:15] Found java - /usr/local/bin/java [05:56:15] Found snpEff - /usr/local/bin/snpEff [05:56:15] Found samclip - /usr/local/bin/samclip [05:56:15] Found seqtk - /usr/local/bin/seqtk [05:56:15] Found parallel - /usr/local/bin/parallel [05:56:15] Found freebayes - /usr/local/bin/freebayes [05:56:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:56:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:56:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:56:15] Found vcfuniq - /usr/local/bin/vcfuniq [05:56:15] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:56:15] Found gzip - /bin/gzip [05:56:15] Found vt - /usr/local/bin/vt [05:56:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:56:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:56:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:56:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:56:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:56:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:56:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:56:17] Using reference: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat [05:56:17] Treating reference as 'fasta' format. [05:56:17] Will use 1 CPU cores. [05:56:17] Using read file: /corral4/main/objects/4/7/9/dataset_479374ce-f6f8-4112-9293-78fcdc1cb420.dat [05:56:17] Creating folder: GCF_002447275_1_ASM244727v1_genomic_fna [05:56:17] Changing working directory: GCF_002447275_1_ASM244727v1_genomic_fna [05:56:17] Creating reference folder: reference [05:56:17] Extracting FASTA and GFF from reference. [05:56:17] Wrote 1 sequences to ref.fa [05:56:17] Wrote 0 features to ref.gff [05:56:17] Shredding /corral4/main/objects/4/7/9/dataset_479374ce-f6f8-4112-9293-78fcdc1cb420.dat into pseudo-reads [05:56:23] Wrote 352954 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [05:56:23] Freebayes will process 1 chunks of 4485121 bp, 1 chunks at a time. [05:56:23] Using BAM RG (Read Group) ID: GCF_002447275_1_ASM244727v1_genomic_fna [05:56:23] Running: samtools faidx reference/ref.fa 2>> snps.log [05:56:23] Running: bwa index reference/ref.fa 2>> snps.log [05:56:28] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [05:56:28] Running: ln -sf reference/ref.fa . 2>> snps.log [05:56:28] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [05:56:28] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [05:56:28] Running: bwa mem -Y -M -R '@RG\tID:GCF_002447275_1_ASM244727v1_genomic_fna\tSM:GCF_002447275_1_ASM244727v1_genomic_fna' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/260/72260554/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/260/72260554/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/260/72260554/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip]
1[05:57:34] This is snippy 4.6.0
Show full stderr[05:57:34] This is snippy 4.6.0 [05:57:34] Written by Torsten Seemann [05:57:34] Obtained from https://github.com/tseemann/snippy [05:57:34] Detected operating system: linux [05:57:34] Enabling bundled linux tools. [05:57:34] Found bwa - /usr/local/bin/bwa [05:57:34] Found bcftools - /usr/local/bin/bcftools [05:57:34] Found samtools - /usr/local/bin/samtools [05:57:34] Found java - /usr/local/bin/java [05:57:34] Found snpEff - /usr/local/bin/snpEff [05:57:34] Found samclip - /usr/local/bin/samclip [05:57:34] Found seqtk - /usr/local/bin/seqtk [05:57:34] Found parallel - /usr/local/bin/parallel [05:57:34] Found freebayes - /usr/local/bin/freebayes [05:57:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:57:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:57:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:57:34] Found vcfuniq - /usr/local/bin/vcfuniq [05:57:34] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:57:34] Found gzip - /bin/gzip [05:57:34] Found vt - /usr/local/bin/vt [05:57:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:57:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:57:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:57:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:57:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:57:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:57:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:57:36] Using reference: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat [05:57:36] Treating reference as 'fasta' format. [05:57:36] Will use 1 CPU cores. [05:57:36] Using read file: /corral4/main/objects/7/7/3/dataset_7738437a-e1ae-4a91-812c-b3134eae84a7.dat [05:57:36] Creating folder: GCA_007989945_1_ASM798994v1_genomic_fna [05:57:36] Changing working directory: GCA_007989945_1_ASM798994v1_genomic_fna [05:57:36] Creating reference folder: reference [05:57:36] Extracting FASTA and GFF from reference. [05:57:36] Wrote 1 sequences to ref.fa [05:57:36] Wrote 0 features to ref.gff [05:57:36] Shredding /corral4/main/objects/7/7/3/dataset_7738437a-e1ae-4a91-812c-b3134eae84a7.dat into pseudo-reads [05:57:43] Wrote 443378 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [05:57:43] Freebayes will process 1 chunks of 4485121 bp, 1 chunks at a time. [05:57:43] Using BAM RG (Read Group) ID: GCA_007989945_1_ASM798994v1_genomic_fna [05:57:43] Running: samtools faidx reference/ref.fa 2>> snps.log [05:57:43] Running: bwa index reference/ref.fa 2>> snps.log [05:57:47] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [05:57:47] Running: ln -sf reference/ref.fa . 2>> snps.log [05:57:47] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [05:57:47] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [05:57:47] Running: bwa mem -Y -M -R '@RG\tID:GCA_007989945_1_ASM798994v1_genomic_fna\tSM:GCA_007989945_1_ASM798994v1_genomic_fna' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/260/72260555/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/260/72260555/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/260/72260555/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip]
1[05:59:02] This is snippy 4.6.0
Show full stderr[05:59:02] This is snippy 4.6.0 [05:59:02] Written by Torsten Seemann [05:59:02] Obtained from https://github.com/tseemann/snippy [05:59:02] Detected operating system: linux [05:59:02] Enabling bundled linux tools. [05:59:02] Found bwa - /usr/local/bin/bwa [05:59:02] Found bcftools - /usr/local/bin/bcftools [05:59:02] Found samtools - /usr/local/bin/samtools [05:59:02] Found java - /usr/local/bin/java [05:59:02] Found snpEff - /usr/local/bin/snpEff [05:59:02] Found samclip - /usr/local/bin/samclip [05:59:02] Found seqtk - /usr/local/bin/seqtk [05:59:02] Found parallel - /usr/local/bin/parallel [05:59:02] Found freebayes - /usr/local/bin/freebayes [05:59:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:59:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:59:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:59:02] Found vcfuniq - /usr/local/bin/vcfuniq [05:59:02] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:59:02] Found gzip - /bin/gzip [05:59:02] Found vt - /usr/local/bin/vt [05:59:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:59:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:59:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:59:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:59:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:59:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:59:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:59:03] Using reference: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat [05:59:03] Treating reference as 'fasta' format. [05:59:03] Will use 1 CPU cores. [05:59:03] Using read file: /corral4/main/objects/8/d/c/dataset_8dce7616-b304-4131-b366-2c3659c915c1.dat [05:59:03] Creating folder: GCF_028583285_1_ASM2858328v1_genomic_fna [05:59:03] Changing working directory: GCF_028583285_1_ASM2858328v1_genomic_fna [05:59:03] Creating reference folder: reference [05:59:03] Extracting FASTA and GFF from reference. [05:59:03] Wrote 1 sequences to ref.fa [05:59:03] Wrote 0 features to ref.gff [05:59:03] Shredding /corral4/main/objects/8/d/c/dataset_8dce7616-b304-4131-b366-2c3659c915c1.dat into pseudo-reads [05:59:06] Wrote 347480 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [05:59:06] Freebayes will process 1 chunks of 4485121 bp, 1 chunks at a time. [05:59:06] Using BAM RG (Read Group) ID: GCF_028583285_1_ASM2858328v1_genomic_fna [05:59:06] Running: samtools faidx reference/ref.fa 2>> snps.log [05:59:06] Running: bwa index reference/ref.fa 2>> snps.log [05:59:07] Error running command, check GCF_028583285_1_ASM2858328v1_genomic_fna/snps.log
1[05:59:52] This is snippy 4.6.0
Show full stderr[05:59:52] This is snippy 4.6.0 [05:59:52] Written by Torsten Seemann [05:59:52] Obtained from https://github.com/tseemann/snippy [05:59:52] Detected operating system: linux [05:59:52] Enabling bundled linux tools. [05:59:52] Found bwa - /usr/local/bin/bwa [05:59:52] Found bcftools - /usr/local/bin/bcftools [05:59:52] Found samtools - /usr/local/bin/samtools [05:59:52] Found java - /usr/local/bin/java [05:59:52] Found snpEff - /usr/local/bin/snpEff [05:59:52] Found samclip - /usr/local/bin/samclip [05:59:52] Found seqtk - /usr/local/bin/seqtk [05:59:52] Found parallel - /usr/local/bin/parallel [05:59:52] Found freebayes - /usr/local/bin/freebayes [05:59:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:59:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:59:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:59:52] Found vcfuniq - /usr/local/bin/vcfuniq [05:59:52] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:59:52] Found gzip - /bin/gzip [05:59:52] Found vt - /usr/local/bin/vt [05:59:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:59:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:59:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:59:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:59:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:59:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:59:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:59:53] Using reference: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat [05:59:53] Treating reference as 'fasta' format. [05:59:53] Will use 1 CPU cores. [05:59:53] Using read file: /corral4/main/objects/e/4/5/dataset_e45e5d48-2705-4eb4-a604-0eba278aadf1.dat [05:59:53] Creating folder: GCF_903992765_1_Q1141_genomic_fna [05:59:53] Changing working directory: GCF_903992765_1_Q1141_genomic_fna [05:59:53] Creating reference folder: reference [05:59:53] Extracting FASTA and GFF from reference. [05:59:53] Wrote 1 sequences to ref.fa [05:59:53] Wrote 0 features to ref.gff [05:59:53] Shredding /corral4/main/objects/e/4/5/dataset_e45e5d48-2705-4eb4-a604-0eba278aadf1.dat into pseudo-reads [05:59:57] Wrote 353492 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [05:59:57] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time. [05:59:57] Using BAM RG (Read Group) ID: GCF_903992765_1_Q1141_genomic_fna [05:59:57] Running: samtools faidx reference/ref.fa 2>> snps.log [05:59:57] Error running command, check GCF_903992765_1_Q1141_genomic_fna/snps.log
1[06:00:26] This is snippy 4.6.0
Show full stderr[06:00:26] This is snippy 4.6.0 [06:00:26] Written by Torsten Seemann [06:00:26] Obtained from https://github.com/tseemann/snippy [06:00:26] Detected operating system: linux [06:00:26] Enabling bundled linux tools. [06:00:26] Found bwa - /usr/local/bin/bwa [06:00:26] Found bcftools - /usr/local/bin/bcftools [06:00:26] Found samtools - /usr/local/bin/samtools [06:00:26] Found java - /usr/local/bin/java [06:00:26] Found snpEff - /usr/local/bin/snpEff [06:00:26] Found samclip - /usr/local/bin/samclip [06:00:26] Found seqtk - /usr/local/bin/seqtk [06:00:26] Found parallel - /usr/local/bin/parallel [06:00:26] Found freebayes - /usr/local/bin/freebayes [06:00:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:00:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:00:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:00:26] Found vcfuniq - /usr/local/bin/vcfuniq [06:00:26] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:00:26] Found gzip - /bin/gzip [06:00:26] Found vt - /usr/local/bin/vt [06:00:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:00:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:00:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:00:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:00:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:00:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:00:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:00:26] Using reference: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat [06:00:26] Treating reference as 'fasta' format. [06:00:26] Will use 1 CPU cores. [06:00:27] Using read file: /corral4/main/objects/4/1/5/dataset_415e26e2-7ee6-4697-9f0c-796e1a5722b6.dat [06:00:27] Creating folder: GCF_902506675_1_P9978_genomic_fna [06:00:27] Changing working directory: GCF_902506675_1_P9978_genomic_fna [06:00:27] Creating reference folder: reference [06:00:27] Extracting FASTA and GFF from reference. [06:00:27] Wrote 1 sequences to ref.fa [06:00:27] Wrote 0 features to ref.gff [06:00:27] Shredding /corral4/main/objects/4/1/5/dataset_415e26e2-7ee6-4697-9f0c-796e1a5722b6.dat into pseudo-reads [06:00:30] Wrote 349272 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [06:00:30] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time. [06:00:30] Using BAM RG (Read Group) ID: GCF_902506675_1_P9978_genomic_fna [06:00:30] Running: samtools faidx reference/ref.fa 2>> snps.log [06:00:30] Error running command, check GCF_902506675_1_P9978_genomic_fna/snps.log
1[06:00:13] This is snippy 4.6.0
Show full stderr[06:00:13] This is snippy 4.6.0 [06:00:13] Written by Torsten Seemann [06:00:13] Obtained from https://github.com/tseemann/snippy [06:00:13] Detected operating system: linux [06:00:13] Enabling bundled linux tools. [06:00:13] Found bwa - /usr/local/bin/bwa [06:00:13] Found bcftools - /usr/local/bin/bcftools [06:00:13] Found samtools - /usr/local/bin/samtools [06:00:13] Found java - /usr/local/bin/java [06:00:13] Found snpEff - /usr/local/bin/snpEff [06:00:13] Found samclip - /usr/local/bin/samclip [06:00:13] Found seqtk - /usr/local/bin/seqtk [06:00:13] Found parallel - /usr/local/bin/parallel [06:00:13] Found freebayes - /usr/local/bin/freebayes [06:00:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:00:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:00:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:00:13] Found vcfuniq - /usr/local/bin/vcfuniq [06:00:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:00:13] Found gzip - /bin/gzip [06:00:13] Found vt - /usr/local/bin/vt [06:00:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:00:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:00:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:00:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:00:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:00:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:00:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:00:14] Using reference: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat [06:00:14] Treating reference as 'fasta' format. [06:00:14] Will use 1 CPU cores. [06:00:15] Using read file: /corral4/main/objects/f/9/9/dataset_f995321f-8b51-4ecb-805f-86b0ba5540fe.dat [06:00:15] Creating folder: GCF_902506635_1_P9981_genomic_fna [06:00:15] Changing working directory: GCF_902506635_1_P9981_genomic_fna [06:00:15] Creating reference folder: reference [06:00:15] Extracting FASTA and GFF from reference. [06:00:15] Wrote 1 sequences to ref.fa [06:00:15] Wrote 0 features to ref.gff [06:00:15] Shredding /corral4/main/objects/f/9/9/dataset_f995321f-8b51-4ecb-805f-86b0ba5540fe.dat into pseudo-reads [06:00:18] Wrote 348054 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [06:00:18] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time. [06:00:18] Using BAM RG (Read Group) ID: GCF_902506635_1_P9981_genomic_fna [06:00:18] Running: samtools faidx reference/ref.fa 2>> snps.log [06:00:18] Error running command, check GCF_902506635_1_P9981_genomic_fna/snps.log
1[06:00:33] This is snippy 4.6.0
Show full stderr[06:00:33] This is snippy 4.6.0 [06:00:33] Written by Torsten Seemann [06:00:33] Obtained from https://github.com/tseemann/snippy [06:00:33] Detected operating system: linux [06:00:33] Enabling bundled linux tools. [06:00:33] Found bwa - /usr/local/bin/bwa [06:00:33] Found bcftools - /usr/local/bin/bcftools [06:00:33] Found samtools - /usr/local/bin/samtools [06:00:33] Found java - /usr/local/bin/java [06:00:33] Found snpEff - /usr/local/bin/snpEff [06:00:33] Found samclip - /usr/local/bin/samclip [06:00:33] Found seqtk - /usr/local/bin/seqtk [06:00:33] Found parallel - /usr/local/bin/parallel [06:00:33] Found freebayes - /usr/local/bin/freebayes [06:00:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:00:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:00:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:00:33] Found vcfuniq - /usr/local/bin/vcfuniq [06:00:33] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:00:33] Found gzip - /bin/gzip [06:00:33] Found vt - /usr/local/bin/vt [06:00:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:00:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:00:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:00:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:00:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:00:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:00:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:00:34] Using reference: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat [06:00:34] Treating reference as 'fasta' format. [06:00:34] Will use 1 CPU cores. [06:00:34] Using read file: /corral4/main/objects/f/4/a/dataset_f4a300b2-ef58-46df-814b-98824da69192.dat [06:00:34] Creating folder: GCF_011392525_1_ASM1139252v1_genomic_fna [06:00:34] Changing working directory: GCF_011392525_1_ASM1139252v1_genomic_fna [06:00:34] Creating reference folder: reference [06:00:34] Extracting FASTA and GFF from reference. [06:00:34] Wrote 1 sequences to ref.fa [06:00:34] Wrote 0 features to ref.gff [06:00:34] Shredding /corral4/main/objects/f/4/a/dataset_f4a300b2-ef58-46df-814b-98824da69192.dat into pseudo-reads [06:00:37] Wrote 365008 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [06:00:37] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time. [06:00:37] Using BAM RG (Read Group) ID: GCF_011392525_1_ASM1139252v1_genomic_fna [06:00:37] Running: samtools faidx reference/ref.fa 2>> snps.log [06:00:37] Error running command, check GCF_011392525_1_ASM1139252v1_genomic_fna/snps.log
1[06:00:29] This is snippy 4.6.0
Show full stderr[06:00:29] This is snippy 4.6.0 [06:00:29] Written by Torsten Seemann [06:00:29] Obtained from https://github.com/tseemann/snippy [06:00:29] Detected operating system: linux [06:00:29] Enabling bundled linux tools. [06:00:29] Found bwa - /usr/local/bin/bwa [06:00:29] Found bcftools - /usr/local/bin/bcftools [06:00:29] Found samtools - /usr/local/bin/samtools [06:00:29] Found java - /usr/local/bin/java [06:00:29] Found snpEff - /usr/local/bin/snpEff [06:00:29] Found samclip - /usr/local/bin/samclip [06:00:29] Found seqtk - /usr/local/bin/seqtk [06:00:29] Found parallel - /usr/local/bin/parallel [06:00:29] Found freebayes - /usr/local/bin/freebayes [06:00:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:00:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:00:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:00:29] Found vcfuniq - /usr/local/bin/vcfuniq [06:00:29] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:00:29] Found gzip - /bin/gzip [06:00:29] Found vt - /usr/local/bin/vt [06:00:29] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:00:29] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:00:29] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:00:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:00:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:00:30] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:00:30] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:00:30] Using reference: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat [06:00:30] Treating reference as 'fasta' format. [06:00:30] Will use 1 CPU cores. [06:00:30] Using read file: /corral4/main/objects/e/9/7/dataset_e97c768b-202c-4835-a61e-ec62a693b7f2.dat [06:00:30] Creating folder: GCF_008033095_1_ASM803309v1_genomic_fna [06:00:30] Changing working directory: GCF_008033095_1_ASM803309v1_genomic_fna [06:00:30] Creating reference folder: reference [06:00:30] Extracting FASTA and GFF from reference. [06:00:30] Wrote 1 sequences to ref.fa [06:00:30] Wrote 0 features to ref.gff [06:00:30] Shredding /corral4/main/objects/e/9/7/dataset_e97c768b-202c-4835-a61e-ec62a693b7f2.dat into pseudo-reads [06:00:33] Wrote 348034 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [06:00:33] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time. [06:00:33] Using BAM RG (Read Group) ID: GCF_008033095_1_ASM803309v1_genomic_fna [06:00:33] Running: samtools faidx reference/ref.fa 2>> snps.log [06:00:33] Error running command, check GCF_008033095_1_ASM803309v1_genomic_fna/snps.log
1[07:02:28] This is snippy 4.6.0
Show full stderr[07:02:28] This is snippy 4.6.0 [07:02:28] Written by Torsten Seemann [07:02:28] Obtained from https://github.com/tseemann/snippy [07:02:28] Detected operating system: linux [07:02:28] Enabling bundled linux tools. [07:02:28] Found bwa - /usr/local/bin/bwa [07:02:28] Found bcftools - /usr/local/bin/bcftools [07:02:28] Found samtools - /usr/local/bin/samtools [07:02:28] Found java - /usr/local/bin/java [07:02:28] Found snpEff - /usr/local/bin/snpEff [07:02:28] Found samclip - /usr/local/bin/samclip [07:02:28] Found seqtk - /usr/local/bin/seqtk [07:02:28] Found parallel - /usr/local/bin/parallel [07:02:28] Found freebayes - /usr/local/bin/freebayes [07:02:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:02:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:02:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:02:28] Found vcfuniq - /usr/local/bin/vcfuniq [07:02:28] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:02:28] Found gzip - /bin/gzip [07:02:28] Found vt - /usr/local/bin/vt [07:02:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:02:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:02:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:02:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:02:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:02:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:02:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:02:29] Using reference: /corral4/main/objects/b/c/7/dataset_bc72f994-0ee8-49f5-b32a-d0eb5858fef9.dat [07:02:29] Treating reference as 'fasta' format. [07:02:29] Will use 1 CPU cores. [07:02:29] Using read file: /corral4/main/objects/3/9/7/dataset_3976135c-0036-4694-8aea-44389097c194.dat [07:02:29] Creating folder: BVBRC_genome_sequence__83__fasta [07:02:29] Changing working directory: BVBRC_genome_sequence__83__fasta [07:02:29] Creating reference folder: reference [07:02:29] Extracting FASTA and GFF from reference. [07:02:29] Wrote 1 sequences to ref.fa [07:02:29] Wrote 0 features to ref.gff [07:02:29] Shredding /corral4/main/objects/3/9/7/dataset_3976135c-0036-4694-8aea-44389097c194.dat into pseudo-reads [07:02:31] Wrote 219558 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [07:02:31] Freebayes will process 1 chunks of 2868471 bp, 1 chunks at a time. [07:02:31] Using BAM RG (Read Group) ID: BVBRC_genome_sequence__83__fasta [07:02:31] Running: samtools faidx reference/ref.fa 2>> snps.log [07:02:31] Running: bwa index reference/ref.fa 2>> snps.log [07:02:32] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [07:02:32] Running: ln -sf reference/ref.fa . 2>> snps.log [07:02:32] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [07:02:32] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [07:02:32] Running: bwa mem -Y -M -R '@RG\tID:BVBRC_genome_sequence__83__fasta\tSM:BVBRC_genome_sequence__83__fasta' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/261/72261288/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/261/72261288/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/261/72261288/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [s
1[07:05:17] This is snippy 4.6.0
Show full stderr[07:05:17] This is snippy 4.6.0 [07:05:17] Written by Torsten Seemann [07:05:17] Obtained from https://github.com/tseemann/snippy [07:05:17] Detected operating system: linux [07:05:17] Enabling bundled linux tools. [07:05:17] Found bwa - /usr/local/bin/bwa [07:05:17] Found bcftools - /usr/local/bin/bcftools [07:05:17] Found samtools - /usr/local/bin/samtools [07:05:17] Found java - /usr/local/bin/java [07:05:17] Found snpEff - /usr/local/bin/snpEff [07:05:17] Found samclip - /usr/local/bin/samclip [07:05:17] Found seqtk - /usr/local/bin/seqtk [07:05:17] Found parallel - /usr/local/bin/parallel [07:05:17] Found freebayes - /usr/local/bin/freebayes [07:05:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:05:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:05:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:05:17] Found vcfuniq - /usr/local/bin/vcfuniq [07:05:17] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:05:17] Found gzip - /bin/gzip [07:05:17] Found vt - /usr/local/bin/vt [07:05:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:05:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:05:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:05:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:05:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:05:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:05:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:05:18] Using reference: /corral4/main/objects/b/c/7/dataset_bc72f994-0ee8-49f5-b32a-d0eb5858fef9.dat [07:05:18] Treating reference as 'fasta' format. [07:05:18] Will use 1 CPU cores. [07:05:18] Using read file: /corral4/main/objects/2/f/9/dataset_2f99f301-ceb0-46ae-9329-f84db170cf49.dat [07:05:18] Creating folder: BVBRC_genome_sequence___2025_10_25T135706_786_fasta [07:05:18] Changing working directory: BVBRC_genome_sequence___2025_10_25T135706_786_fasta [07:05:18] Creating reference folder: reference [07:05:18] Extracting FASTA and GFF from reference. [07:05:18] Wrote 1 sequences to ref.fa [07:05:18] Wrote 0 features to ref.gff [07:05:18] Shredding /corral4/main/objects/2/f/9/dataset_2f99f301-ceb0-46ae-9329-f84db170cf49.dat into pseudo-reads [07:05:20] Wrote 236178 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [07:05:20] Freebayes will process 1 chunks of 2868471 bp, 1 chunks at a time. [07:05:20] Using BAM RG (Read Group) ID: BVBRC_genome_sequence___2025_10_25T135706_786_fasta [07:05:20] Running: samtools faidx reference/ref.fa 2>> snps.log [07:05:20] Running: bwa index reference/ref.fa 2>> snps.log [07:05:22] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [07:05:22] Running: ln -sf reference/ref.fa . 2>> snps.log [07:05:22] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [07:05:22] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [07:05:22] Running: bwa mem -Y -M -R '@RG\tID:BVBRC_genome_sequence___2025_10_25T135706_786_fasta\tSM:BVBRC_genome_sequence___2025_10_25T135706_786_fasta' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/261/72261363/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/261/72261363/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/261/72261363/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samcl
1[07:05:35] This is snippy 4.6.0
Show full stderr[07:05:35] This is snippy 4.6.0 [07:05:35] Written by Torsten Seemann [07:05:35] Obtained from https://github.com/tseemann/snippy [07:05:35] Detected operating system: linux [07:05:35] Enabling bundled linux tools. [07:05:35] Found bwa - /usr/local/bin/bwa [07:05:35] Found bcftools - /usr/local/bin/bcftools [07:05:35] Found samtools - /usr/local/bin/samtools [07:05:35] Found java - /usr/local/bin/java [07:05:35] Found snpEff - /usr/local/bin/snpEff [07:05:35] Found samclip - /usr/local/bin/samclip [07:05:35] Found seqtk - /usr/local/bin/seqtk [07:05:35] Found parallel - /usr/local/bin/parallel [07:05:35] Found freebayes - /usr/local/bin/freebayes [07:05:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:05:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:05:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:05:35] Found vcfuniq - /usr/local/bin/vcfuniq [07:05:35] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:05:35] Found gzip - /bin/gzip [07:05:35] Found vt - /usr/local/bin/vt [07:05:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:05:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:05:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:05:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:05:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:05:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:05:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:05:36] Using reference: /corral4/main/objects/b/c/7/dataset_bc72f994-0ee8-49f5-b32a-d0eb5858fef9.dat [07:05:36] Treating reference as 'fasta' format. [07:05:36] Will use 1 CPU cores. [07:05:36] Using read file: /corral4/main/objects/b/0/9/dataset_b09d551a-c85b-4b80-9753-ef6046602025.dat [07:05:36] Creating folder: BVBRC_genome_sequence__11__fasta [07:05:36] Changing working directory: BVBRC_genome_sequence__11__fasta [07:05:36] Creating reference folder: reference [07:05:36] Extracting FASTA and GFF from reference. [07:05:36] Wrote 1 sequences to ref.fa [07:05:36] Wrote 0 features to ref.gff [07:05:36] Shredding /corral4/main/objects/b/0/9/dataset_b09d551a-c85b-4b80-9753-ef6046602025.dat into pseudo-reads [07:05:38] Wrote 221348 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [07:05:38] Freebayes will process 1 chunks of 2868471 bp, 1 chunks at a time. [07:05:38] Using BAM RG (Read Group) ID: BVBRC_genome_sequence__11__fasta [07:05:38] Running: samtools faidx reference/ref.fa 2>> snps.log [07:05:38] Running: bwa index reference/ref.fa 2>> snps.log [07:05:39] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [07:05:40] Running: ln -sf reference/ref.fa . 2>> snps.log [07:05:40] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [07:05:40] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [07:05:40] Running: bwa mem -Y -M -R '@RG\tID:BVBRC_genome_sequence__11__fasta\tSM:BVBRC_genome_sequence__11__fasta' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/261/72261397/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/261/72261397/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/261/72261397/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [s
1[06:48:17] This is snippy 4.6.0
Show full stderr[06:48:17] This is snippy 4.6.0 [06:48:17] Written by Torsten Seemann [06:48:17] Obtained from https://github.com/tseemann/snippy [06:48:17] Detected operating system: linux [06:48:17] Enabling bundled linux tools. [06:48:17] Found bwa - /usr/local/bin/bwa [06:48:17] Found bcftools - /usr/local/bin/bcftools [06:48:17] Found samtools - /usr/local/bin/samtools [06:48:17] Found java - /usr/local/bin/java [06:48:17] Found snpEff - /usr/local/bin/snpEff [06:48:17] Found samclip - /usr/local/bin/samclip [06:48:17] Found seqtk - /usr/local/bin/seqtk [06:48:17] Found parallel - /usr/local/bin/parallel [06:48:17] Found freebayes - /usr/local/bin/freebayes [06:48:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:48:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:48:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:48:17] Found vcfuniq - /usr/local/bin/vcfuniq [06:48:17] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:48:17] Found gzip - /bin/gzip [06:48:17] Found vt - /usr/local/bin/vt [06:48:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:48:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:48:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:48:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:48:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:48:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:48:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:48:18] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:49:00] This is snippy 4.6.0
Show full stderr[06:49:00] This is snippy 4.6.0 [06:49:00] Written by Torsten Seemann [06:49:00] Obtained from https://github.com/tseemann/snippy [06:49:00] Detected operating system: linux [06:49:00] Enabling bundled linux tools. [06:49:00] Found bwa - /usr/local/bin/bwa [06:49:00] Found bcftools - /usr/local/bin/bcftools [06:49:00] Found samtools - /usr/local/bin/samtools [06:49:00] Found java - /usr/local/bin/java [06:49:00] Found snpEff - /usr/local/bin/snpEff [06:49:00] Found samclip - /usr/local/bin/samclip [06:49:00] Found seqtk - /usr/local/bin/seqtk [06:49:00] Found parallel - /usr/local/bin/parallel [06:49:00] Found freebayes - /usr/local/bin/freebayes [06:49:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:49:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:49:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:49:00] Found vcfuniq - /usr/local/bin/vcfuniq [06:49:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:49:00] Found gzip - /bin/gzip [06:49:00] Found vt - /usr/local/bin/vt [06:49:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:49:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:49:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:49:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:49:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:49:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:49:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:49:01] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:00:39] This is snippy 4.6.0
Show full stderr[07:00:39] This is snippy 4.6.0 [07:00:39] Written by Torsten Seemann [07:00:39] Obtained from https://github.com/tseemann/snippy [07:00:39] Detected operating system: linux [07:00:39] Enabling bundled linux tools. [07:00:39] Found bwa - /usr/local/bin/bwa [07:00:39] Found bcftools - /usr/local/bin/bcftools [07:00:39] Found samtools - /usr/local/bin/samtools [07:00:39] Found java - /usr/local/bin/java [07:00:39] Found snpEff - /usr/local/bin/snpEff [07:00:39] Found samclip - /usr/local/bin/samclip [07:00:39] Found seqtk - /usr/local/bin/seqtk [07:00:39] Found parallel - /usr/local/bin/parallel [07:00:39] Found freebayes - /usr/local/bin/freebayes [07:00:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:00:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:00:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:00:39] Found vcfuniq - /usr/local/bin/vcfuniq [07:00:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:00:39] Found gzip - /bin/gzip [07:00:39] Found vt - /usr/local/bin/vt [07:00:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:00:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:00:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:00:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:00:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:00:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:00:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:00:40] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:06:23] This is snippy 4.6.0
Show full stderr[07:06:23] This is snippy 4.6.0 [07:06:23] Written by Torsten Seemann [07:06:23] Obtained from https://github.com/tseemann/snippy [07:06:23] Detected operating system: linux [07:06:23] Enabling bundled linux tools. [07:06:24] Found bwa - /usr/local/bin/bwa [07:06:24] Found bcftools - /usr/local/bin/bcftools [07:06:24] Found samtools - /usr/local/bin/samtools [07:06:24] Found java - /usr/local/bin/java [07:06:24] Found snpEff - /usr/local/bin/snpEff [07:06:24] Found samclip - /usr/local/bin/samclip [07:06:24] Found seqtk - /usr/local/bin/seqtk [07:06:24] Found parallel - /usr/local/bin/parallel [07:06:24] Found freebayes - /usr/local/bin/freebayes [07:06:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:06:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:06:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:06:24] Found vcfuniq - /usr/local/bin/vcfuniq [07:06:24] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:06:24] Found gzip - /bin/gzip [07:06:24] Found vt - /usr/local/bin/vt [07:06:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:06:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:06:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:06:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:06:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:06:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:06:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:06:24] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:49:33] This is snippy 4.6.0
Show full stderr[06:49:33] This is snippy 4.6.0 [06:49:33] Written by Torsten Seemann [06:49:33] Obtained from https://github.com/tseemann/snippy [06:49:33] Detected operating system: linux [06:49:33] Enabling bundled linux tools. [06:49:33] Found bwa - /usr/local/bin/bwa [06:49:33] Found bcftools - /usr/local/bin/bcftools [06:49:33] Found samtools - /usr/local/bin/samtools [06:49:33] Found java - /usr/local/bin/java [06:49:33] Found snpEff - /usr/local/bin/snpEff [06:49:33] Found samclip - /usr/local/bin/samclip [06:49:33] Found seqtk - /usr/local/bin/seqtk [06:49:33] Found parallel - /usr/local/bin/parallel [06:49:33] Found freebayes - /usr/local/bin/freebayes [06:49:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:49:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:49:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:49:33] Found vcfuniq - /usr/local/bin/vcfuniq [06:49:33] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:49:33] Found gzip - /bin/gzip [06:49:33] Found vt - /usr/local/bin/vt [06:49:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:49:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:49:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:49:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:49:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:49:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:49:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:49:34] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:48:13] This is snippy 4.6.0
Show full stderr[06:48:13] This is snippy 4.6.0 [06:48:13] Written by Torsten Seemann [06:48:13] Obtained from https://github.com/tseemann/snippy [06:48:13] Detected operating system: linux [06:48:13] Enabling bundled linux tools. [06:48:13] Found bwa - /usr/local/bin/bwa [06:48:13] Found bcftools - /usr/local/bin/bcftools [06:48:13] Found samtools - /usr/local/bin/samtools [06:48:13] Found java - /usr/local/bin/java [06:48:13] Found snpEff - /usr/local/bin/snpEff [06:48:13] Found samclip - /usr/local/bin/samclip [06:48:13] Found seqtk - /usr/local/bin/seqtk [06:48:13] Found parallel - /usr/local/bin/parallel [06:48:13] Found freebayes - /usr/local/bin/freebayes [06:48:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:48:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:48:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:48:13] Found vcfuniq - /usr/local/bin/vcfuniq [06:48:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:48:13] Found gzip - /bin/gzip [06:48:13] Found vt - /usr/local/bin/vt [06:48:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:48:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:48:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:48:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:48:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:48:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:48:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:48:14] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:54:26] This is snippy 4.6.0
Show full stderr[06:54:26] This is snippy 4.6.0 [06:54:26] Written by Torsten Seemann [06:54:26] Obtained from https://github.com/tseemann/snippy [06:54:26] Detected operating system: linux [06:54:26] Enabling bundled linux tools. [06:54:26] Found bwa - /usr/local/bin/bwa [06:54:26] Found bcftools - /usr/local/bin/bcftools [06:54:26] Found samtools - /usr/local/bin/samtools [06:54:26] Found java - /usr/local/bin/java [06:54:26] Found snpEff - /usr/local/bin/snpEff [06:54:26] Found samclip - /usr/local/bin/samclip [06:54:26] Found seqtk - /usr/local/bin/seqtk [06:54:26] Found parallel - /usr/local/bin/parallel [06:54:26] Found freebayes - /usr/local/bin/freebayes [06:54:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:54:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:54:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:54:26] Found vcfuniq - /usr/local/bin/vcfuniq [06:54:26] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:54:26] Found gzip - /bin/gzip [06:54:26] Found vt - /usr/local/bin/vt [06:54:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:54:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:54:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:54:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:54:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:54:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:54:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:54:26] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:06:53] This is snippy 4.6.0
Show full stderr[07:06:53] This is snippy 4.6.0 [07:06:53] Written by Torsten Seemann [07:06:53] Obtained from https://github.com/tseemann/snippy [07:06:53] Detected operating system: linux [07:06:53] Enabling bundled linux tools. [07:06:53] Found bwa - /usr/local/bin/bwa [07:06:53] Found bcftools - /usr/local/bin/bcftools [07:06:53] Found samtools - /usr/local/bin/samtools [07:06:53] Found java - /usr/local/bin/java [07:06:53] Found snpEff - /usr/local/bin/snpEff [07:06:53] Found samclip - /usr/local/bin/samclip [07:06:53] Found seqtk - /usr/local/bin/seqtk [07:06:53] Found parallel - /usr/local/bin/parallel [07:06:53] Found freebayes - /usr/local/bin/freebayes [07:06:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:06:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:06:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:06:53] Found vcfuniq - /usr/local/bin/vcfuniq [07:06:53] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:06:53] Found gzip - /bin/gzip [07:06:53] Found vt - /usr/local/bin/vt [07:06:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:06:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:06:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:06:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:06:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:06:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:06:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:06:54] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:07:09] This is snippy 4.6.0
Show full stderr[07:07:09] This is snippy 4.6.0 [07:07:09] Written by Torsten Seemann [07:07:09] Obtained from https://github.com/tseemann/snippy [07:07:09] Detected operating system: linux [07:07:09] Enabling bundled linux tools. [07:07:09] Found bwa - /usr/local/bin/bwa [07:07:09] Found bcftools - /usr/local/bin/bcftools [07:07:09] Found samtools - /usr/local/bin/samtools [07:07:09] Found java - /usr/local/bin/java [07:07:09] Found snpEff - /usr/local/bin/snpEff [07:07:09] Found samclip - /usr/local/bin/samclip [07:07:09] Found seqtk - /usr/local/bin/seqtk [07:07:09] Found parallel - /usr/local/bin/parallel [07:07:09] Found freebayes - /usr/local/bin/freebayes [07:07:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:07:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:07:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:07:09] Found vcfuniq - /usr/local/bin/vcfuniq [07:07:09] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:07:09] Found gzip - /bin/gzip [07:07:09] Found vt - /usr/local/bin/vt [07:07:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:07:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:07:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:07:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:07:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:07:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:07:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:07:10] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:48:09] This is snippy 4.6.0
Show full stderr[06:48:09] This is snippy 4.6.0 [06:48:09] Written by Torsten Seemann [06:48:09] Obtained from https://github.com/tseemann/snippy [06:48:09] Detected operating system: linux [06:48:09] Enabling bundled linux tools. [06:48:09] Found bwa - /usr/local/bin/bwa [06:48:09] Found bcftools - /usr/local/bin/bcftools [06:48:09] Found samtools - /usr/local/bin/samtools [06:48:09] Found java - /usr/local/bin/java [06:48:09] Found snpEff - /usr/local/bin/snpEff [06:48:09] Found samclip - /usr/local/bin/samclip [06:48:10] Found seqtk - /usr/local/bin/seqtk [06:48:10] Found parallel - /usr/local/bin/parallel [06:48:10] Found freebayes - /usr/local/bin/freebayes [06:48:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:48:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:48:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:48:10] Found vcfuniq - /usr/local/bin/vcfuniq [06:48:10] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:48:10] Found gzip - /bin/gzip [06:48:10] Found vt - /usr/local/bin/vt [06:48:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:48:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:48:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:48:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:48:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:48:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:48:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:48:10] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:48:54] This is snippy 4.6.0
Show full stderr[06:48:54] This is snippy 4.6.0 [06:48:54] Written by Torsten Seemann [06:48:54] Obtained from https://github.com/tseemann/snippy [06:48:54] Detected operating system: linux [06:48:54] Enabling bundled linux tools. [06:48:54] Found bwa - /usr/local/bin/bwa [06:48:54] Found bcftools - /usr/local/bin/bcftools [06:48:54] Found samtools - /usr/local/bin/samtools [06:48:54] Found java - /usr/local/bin/java [06:48:54] Found snpEff - /usr/local/bin/snpEff [06:48:54] Found samclip - /usr/local/bin/samclip [06:48:54] Found seqtk - /usr/local/bin/seqtk [06:48:54] Found parallel - /usr/local/bin/parallel [06:48:54] Found freebayes - /usr/local/bin/freebayes [06:48:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:48:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:48:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:48:54] Found vcfuniq - /usr/local/bin/vcfuniq [06:48:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:48:54] Found gzip - /bin/gzip [06:48:54] Found vt - /usr/local/bin/vt [06:48:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:48:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:48:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:48:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:48:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:48:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:48:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:48:55] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:48:57] This is snippy 4.6.0
Show full stderr[06:48:57] This is snippy 4.6.0 [06:48:57] Written by Torsten Seemann [06:48:57] Obtained from https://github.com/tseemann/snippy [06:48:57] Detected operating system: linux [06:48:57] Enabling bundled linux tools. [06:48:57] Found bwa - /usr/local/bin/bwa [06:48:57] Found bcftools - /usr/local/bin/bcftools [06:48:57] Found samtools - /usr/local/bin/samtools [06:48:57] Found java - /usr/local/bin/java [06:48:57] Found snpEff - /usr/local/bin/snpEff [06:48:57] Found samclip - /usr/local/bin/samclip [06:48:57] Found seqtk - /usr/local/bin/seqtk [06:48:57] Found parallel - /usr/local/bin/parallel [06:48:57] Found freebayes - /usr/local/bin/freebayes [06:48:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:48:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:48:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:48:57] Found vcfuniq - /usr/local/bin/vcfuniq [06:48:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:48:57] Found gzip - /bin/gzip [06:48:57] Found vt - /usr/local/bin/vt [06:48:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:48:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:48:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:48:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:48:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:48:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:48:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:48:58] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:59:57] This is snippy 4.6.0
Show full stderr[06:59:57] This is snippy 4.6.0 [06:59:57] Written by Torsten Seemann [06:59:57] Obtained from https://github.com/tseemann/snippy [06:59:57] Detected operating system: linux [06:59:57] Enabling bundled linux tools. [06:59:57] Found bwa - /usr/local/bin/bwa [06:59:57] Found bcftools - /usr/local/bin/bcftools [06:59:57] Found samtools - /usr/local/bin/samtools [06:59:57] Found java - /usr/local/bin/java [06:59:57] Found snpEff - /usr/local/bin/snpEff [06:59:57] Found samclip - /usr/local/bin/samclip [06:59:57] Found seqtk - /usr/local/bin/seqtk [06:59:57] Found parallel - /usr/local/bin/parallel [06:59:57] Found freebayes - /usr/local/bin/freebayes [06:59:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:59:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:59:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:59:57] Found vcfuniq - /usr/local/bin/vcfuniq [06:59:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:59:57] Found gzip - /bin/gzip [06:59:57] Found vt - /usr/local/bin/vt [06:59:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:59:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:59:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:59:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:59:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:59:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:59:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:59:58] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:49:25] This is snippy 4.6.0
Show full stderr[06:49:25] This is snippy 4.6.0 [06:49:25] Written by Torsten Seemann [06:49:25] Obtained from https://github.com/tseemann/snippy [06:49:25] Detected operating system: linux [06:49:25] Enabling bundled linux tools. [06:49:25] Found bwa - /usr/local/bin/bwa [06:49:25] Found bcftools - /usr/local/bin/bcftools [06:49:25] Found samtools - /usr/local/bin/samtools [06:49:25] Found java - /usr/local/bin/java [06:49:25] Found snpEff - /usr/local/bin/snpEff [06:49:25] Found samclip - /usr/local/bin/samclip [06:49:25] Found seqtk - /usr/local/bin/seqtk [06:49:25] Found parallel - /usr/local/bin/parallel [06:49:25] Found freebayes - /usr/local/bin/freebayes [06:49:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:49:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:49:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:49:25] Found vcfuniq - /usr/local/bin/vcfuniq [06:49:25] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:49:25] Found gzip - /bin/gzip [06:49:25] Found vt - /usr/local/bin/vt [06:49:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:49:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:49:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:49:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:49:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:49:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:49:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:49:26] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:07:10] This is snippy 4.6.0
Show full stderr[07:07:10] This is snippy 4.6.0 [07:07:10] Written by Torsten Seemann [07:07:10] Obtained from https://github.com/tseemann/snippy [07:07:10] Detected operating system: linux [07:07:10] Enabling bundled linux tools. [07:07:10] Found bwa - /usr/local/bin/bwa [07:07:10] Found bcftools - /usr/local/bin/bcftools [07:07:10] Found samtools - /usr/local/bin/samtools [07:07:10] Found java - /usr/local/bin/java [07:07:10] Found snpEff - /usr/local/bin/snpEff [07:07:10] Found samclip - /usr/local/bin/samclip [07:07:10] Found seqtk - /usr/local/bin/seqtk [07:07:10] Found parallel - /usr/local/bin/parallel [07:07:10] Found freebayes - /usr/local/bin/freebayes [07:07:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:07:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:07:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:07:10] Found vcfuniq - /usr/local/bin/vcfuniq [07:07:10] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:07:10] Found gzip - /bin/gzip [07:07:10] Found vt - /usr/local/bin/vt [07:07:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:07:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:07:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:07:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:07:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:07:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:07:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:07:11] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:53:56] This is snippy 4.6.0
Show full stderr[06:53:56] This is snippy 4.6.0 [06:53:56] Written by Torsten Seemann [06:53:56] Obtained from https://github.com/tseemann/snippy [06:53:56] Detected operating system: linux [06:53:56] Enabling bundled linux tools. [06:53:56] Found bwa - /usr/local/bin/bwa [06:53:56] Found bcftools - /usr/local/bin/bcftools [06:53:56] Found samtools - /usr/local/bin/samtools [06:53:56] Found java - /usr/local/bin/java [06:53:56] Found snpEff - /usr/local/bin/snpEff [06:53:56] Found samclip - /usr/local/bin/samclip [06:53:56] Found seqtk - /usr/local/bin/seqtk [06:53:56] Found parallel - /usr/local/bin/parallel [06:53:56] Found freebayes - /usr/local/bin/freebayes [06:53:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:53:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:53:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:53:56] Found vcfuniq - /usr/local/bin/vcfuniq [06:53:56] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:53:56] Found gzip - /bin/gzip [06:53:56] Found vt - /usr/local/bin/vt [06:53:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:53:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:53:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:53:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:53:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:53:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:53:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:53:56] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:54:09] This is snippy 4.6.0
Show full stderr[06:54:09] This is snippy 4.6.0 [06:54:09] Written by Torsten Seemann [06:54:09] Obtained from https://github.com/tseemann/snippy [06:54:09] Detected operating system: linux [06:54:09] Enabling bundled linux tools. [06:54:09] Found bwa - /usr/local/bin/bwa [06:54:09] Found bcftools - /usr/local/bin/bcftools [06:54:09] Found samtools - /usr/local/bin/samtools [06:54:09] Found java - /usr/local/bin/java [06:54:09] Found snpEff - /usr/local/bin/snpEff [06:54:09] Found samclip - /usr/local/bin/samclip [06:54:09] Found seqtk - /usr/local/bin/seqtk [06:54:09] Found parallel - /usr/local/bin/parallel [06:54:09] Found freebayes - /usr/local/bin/freebayes [06:54:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:54:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:54:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:54:09] Found vcfuniq - /usr/local/bin/vcfuniq [06:54:09] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:54:09] Found gzip - /bin/gzip [06:54:09] Found vt - /usr/local/bin/vt [06:54:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:54:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:54:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:54:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:54:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:54:09] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:54:09] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:54:09] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:54:06] This is snippy 4.6.0
Show full stderr[06:54:06] This is snippy 4.6.0 [06:54:06] Written by Torsten Seemann [06:54:06] Obtained from https://github.com/tseemann/snippy [06:54:06] Detected operating system: linux [06:54:06] Enabling bundled linux tools. [06:54:06] Found bwa - /usr/local/bin/bwa [06:54:06] Found bcftools - /usr/local/bin/bcftools [06:54:06] Found samtools - /usr/local/bin/samtools [06:54:06] Found java - /usr/local/bin/java [06:54:06] Found snpEff - /usr/local/bin/snpEff [06:54:06] Found samclip - /usr/local/bin/samclip [06:54:06] Found seqtk - /usr/local/bin/seqtk [06:54:06] Found parallel - /usr/local/bin/parallel [06:54:06] Found freebayes - /usr/local/bin/freebayes [06:54:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:54:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:54:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:54:06] Found vcfuniq - /usr/local/bin/vcfuniq [06:54:06] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:54:06] Found gzip - /bin/gzip [06:54:06] Found vt - /usr/local/bin/vt [06:54:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:54:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:54:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:54:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:54:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:54:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:54:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:54:06] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:48:44] This is snippy 4.6.0
Show full stderr[06:48:44] This is snippy 4.6.0 [06:48:44] Written by Torsten Seemann [06:48:44] Obtained from https://github.com/tseemann/snippy [06:48:44] Detected operating system: linux [06:48:44] Enabling bundled linux tools. [06:48:44] Found bwa - /usr/local/bin/bwa [06:48:44] Found bcftools - /usr/local/bin/bcftools [06:48:44] Found samtools - /usr/local/bin/samtools [06:48:44] Found java - /usr/local/bin/java [06:48:44] Found snpEff - /usr/local/bin/snpEff [06:48:44] Found samclip - /usr/local/bin/samclip [06:48:44] Found seqtk - /usr/local/bin/seqtk [06:48:44] Found parallel - /usr/local/bin/parallel [06:48:44] Found freebayes - /usr/local/bin/freebayes [06:48:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:48:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:48:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:48:44] Found vcfuniq - /usr/local/bin/vcfuniq [06:48:44] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:48:44] Found gzip - /bin/gzip [06:48:44] Found vt - /usr/local/bin/vt [06:48:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:48:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:48:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:48:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:48:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:48:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:48:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:48:45] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:12:20] This is snippy 4.6.0
Show full stderr[07:12:20] This is snippy 4.6.0 [07:12:20] Written by Torsten Seemann [07:12:20] Obtained from https://github.com/tseemann/snippy [07:12:20] Detected operating system: linux [07:12:20] Enabling bundled linux tools. [07:12:20] Found bwa - /usr/local/bin/bwa [07:12:20] Found bcftools - /usr/local/bin/bcftools [07:12:20] Found samtools - /usr/local/bin/samtools [07:12:20] Found java - /usr/local/bin/java [07:12:20] Found snpEff - /usr/local/bin/snpEff [07:12:20] Found samclip - /usr/local/bin/samclip [07:12:20] Found seqtk - /usr/local/bin/seqtk [07:12:20] Found parallel - /usr/local/bin/parallel [07:12:20] Found freebayes - /usr/local/bin/freebayes [07:12:20] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:12:20] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:12:20] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:12:20] Found vcfuniq - /usr/local/bin/vcfuniq [07:12:20] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:12:20] Found gzip - /bin/gzip [07:12:20] Found vt - /usr/local/bin/vt [07:12:20] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:12:20] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:12:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:12:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:12:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:12:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:12:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:12:21] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:12:44] This is snippy 4.6.0
Show full stderr[07:12:44] This is snippy 4.6.0 [07:12:44] Written by Torsten Seemann [07:12:44] Obtained from https://github.com/tseemann/snippy [07:12:44] Detected operating system: linux [07:12:44] Enabling bundled linux tools. [07:12:44] Found bwa - /usr/local/bin/bwa [07:12:44] Found bcftools - /usr/local/bin/bcftools [07:12:44] Found samtools - /usr/local/bin/samtools [07:12:44] Found java - /usr/local/bin/java [07:12:44] Found snpEff - /usr/local/bin/snpEff [07:12:44] Found samclip - /usr/local/bin/samclip [07:12:44] Found seqtk - /usr/local/bin/seqtk [07:12:44] Found parallel - /usr/local/bin/parallel [07:12:44] Found freebayes - /usr/local/bin/freebayes [07:12:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:12:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:12:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:12:44] Found vcfuniq - /usr/local/bin/vcfuniq [07:12:44] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:12:44] Found gzip - /bin/gzip [07:12:44] Found vt - /usr/local/bin/vt [07:12:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:12:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:12:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:12:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:12:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:12:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:12:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:12:45] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:19:00] This is snippy 4.6.0
Show full stderr[07:19:00] This is snippy 4.6.0 [07:19:00] Written by Torsten Seemann [07:19:00] Obtained from https://github.com/tseemann/snippy [07:19:00] Detected operating system: linux [07:19:00] Enabling bundled linux tools. [07:19:00] Found bwa - /usr/local/bin/bwa [07:19:00] Found bcftools - /usr/local/bin/bcftools [07:19:00] Found samtools - /usr/local/bin/samtools [07:19:00] Found java - /usr/local/bin/java [07:19:00] Found snpEff - /usr/local/bin/snpEff [07:19:00] Found samclip - /usr/local/bin/samclip [07:19:00] Found seqtk - /usr/local/bin/seqtk [07:19:00] Found parallel - /usr/local/bin/parallel [07:19:00] Found freebayes - /usr/local/bin/freebayes [07:19:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:19:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:19:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:19:00] Found vcfuniq - /usr/local/bin/vcfuniq [07:19:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:19:00] Found gzip - /bin/gzip [07:19:00] Found vt - /usr/local/bin/vt [07:19:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:19:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:19:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:19:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:19:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:19:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:19:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:19:00] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:19:44] This is snippy 4.6.0
Show full stderr[07:19:44] This is snippy 4.6.0 [07:19:44] Written by Torsten Seemann [07:19:44] Obtained from https://github.com/tseemann/snippy [07:19:44] Detected operating system: linux [07:19:44] Enabling bundled linux tools. [07:19:44] Found bwa - /usr/local/bin/bwa [07:19:44] Found bcftools - /usr/local/bin/bcftools [07:19:44] Found samtools - /usr/local/bin/samtools [07:19:44] Found java - /usr/local/bin/java [07:19:44] Found snpEff - /usr/local/bin/snpEff [07:19:44] Found samclip - /usr/local/bin/samclip [07:19:44] Found seqtk - /usr/local/bin/seqtk [07:19:44] Found parallel - /usr/local/bin/parallel [07:19:44] Found freebayes - /usr/local/bin/freebayes [07:19:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:19:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:19:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:19:44] Found vcfuniq - /usr/local/bin/vcfuniq [07:19:44] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:19:44] Found gzip - /bin/gzip [07:19:44] Found vt - /usr/local/bin/vt [07:19:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:19:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:19:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:19:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:19:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:19:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:19:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:19:45] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:49:39] This is snippy 4.6.0
Show full stderr[06:49:39] This is snippy 4.6.0 [06:49:39] Written by Torsten Seemann [06:49:39] Obtained from https://github.com/tseemann/snippy [06:49:39] Detected operating system: linux [06:49:39] Enabling bundled linux tools. [06:49:39] Found bwa - /usr/local/bin/bwa [06:49:39] Found bcftools - /usr/local/bin/bcftools [06:49:39] Found samtools - /usr/local/bin/samtools [06:49:39] Found java - /usr/local/bin/java [06:49:39] Found snpEff - /usr/local/bin/snpEff [06:49:39] Found samclip - /usr/local/bin/samclip [06:49:39] Found seqtk - /usr/local/bin/seqtk [06:49:39] Found parallel - /usr/local/bin/parallel [06:49:39] Found freebayes - /usr/local/bin/freebayes [06:49:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:49:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:49:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:49:39] Found vcfuniq - /usr/local/bin/vcfuniq [06:49:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:49:39] Found gzip - /bin/gzip [06:49:39] Found vt - /usr/local/bin/vt [06:49:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:49:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:49:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:49:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:49:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:49:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:49:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:49:40] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:26:47] This is snippy 4.6.0
Show full stderr[07:26:47] This is snippy 4.6.0 [07:26:47] Written by Torsten Seemann [07:26:47] Obtained from https://github.com/tseemann/snippy [07:26:47] Detected operating system: linux [07:26:47] Enabling bundled linux tools. [07:26:47] Found bwa - /usr/local/bin/bwa [07:26:47] Found bcftools - /usr/local/bin/bcftools [07:26:47] Found samtools - /usr/local/bin/samtools [07:26:47] Found java - /usr/local/bin/java [07:26:47] Found snpEff - /usr/local/bin/snpEff [07:26:47] Found samclip - /usr/local/bin/samclip [07:26:47] Found seqtk - /usr/local/bin/seqtk [07:26:47] Found parallel - /usr/local/bin/parallel [07:26:47] Found freebayes - /usr/local/bin/freebayes [07:26:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:26:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:26:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:26:48] Found vcfuniq - /usr/local/bin/vcfuniq [07:26:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:26:48] Found gzip - /bin/gzip [07:26:48] Found vt - /usr/local/bin/vt [07:26:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:26:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:26:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:26:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:26:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:26:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:26:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:26:48] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:31:56] This is snippy 4.6.0
Show full stderr[07:31:56] This is snippy 4.6.0 [07:31:56] Written by Torsten Seemann [07:31:56] Obtained from https://github.com/tseemann/snippy [07:31:56] Detected operating system: linux [07:31:56] Enabling bundled linux tools. [07:31:56] Found bwa - /usr/local/bin/bwa [07:31:56] Found bcftools - /usr/local/bin/bcftools [07:31:56] Found samtools - /usr/local/bin/samtools [07:31:56] Found java - /usr/local/bin/java [07:31:56] Found snpEff - /usr/local/bin/snpEff [07:31:56] Found samclip - /usr/local/bin/samclip [07:31:56] Found seqtk - /usr/local/bin/seqtk [07:31:56] Found parallel - /usr/local/bin/parallel [07:31:56] Found freebayes - /usr/local/bin/freebayes [07:31:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:31:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:31:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:31:56] Found vcfuniq - /usr/local/bin/vcfuniq [07:31:56] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:31:56] Found gzip - /bin/gzip [07:31:56] Found vt - /usr/local/bin/vt [07:31:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:31:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:31:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:31:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:31:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:31:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:31:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:31:57] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:48:30] This is snippy 4.6.0
Show full stderr[06:48:30] This is snippy 4.6.0 [06:48:30] Written by Torsten Seemann [06:48:30] Obtained from https://github.com/tseemann/snippy [06:48:30] Detected operating system: linux [06:48:30] Enabling bundled linux tools. [06:48:30] Found bwa - /usr/local/bin/bwa [06:48:30] Found bcftools - /usr/local/bin/bcftools [06:48:30] Found samtools - /usr/local/bin/samtools [06:48:30] Found java - /usr/local/bin/java [06:48:30] Found snpEff - /usr/local/bin/snpEff [06:48:30] Found samclip - /usr/local/bin/samclip [06:48:30] Found seqtk - /usr/local/bin/seqtk [06:48:30] Found parallel - /usr/local/bin/parallel [06:48:30] Found freebayes - /usr/local/bin/freebayes [06:48:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:48:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:48:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:48:30] Found vcfuniq - /usr/local/bin/vcfuniq [06:48:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:48:30] Found gzip - /bin/gzip [06:48:30] Found vt - /usr/local/bin/vt [06:48:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:48:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:48:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:48:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:48:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:48:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:48:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:48:31] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:19:26] This is snippy 4.6.0
Show full stderr[07:19:26] This is snippy 4.6.0 [07:19:26] Written by Torsten Seemann [07:19:26] Obtained from https://github.com/tseemann/snippy [07:19:26] Detected operating system: linux [07:19:26] Enabling bundled linux tools. [07:19:26] Found bwa - /usr/local/bin/bwa [07:19:26] Found bcftools - /usr/local/bin/bcftools [07:19:26] Found samtools - /usr/local/bin/samtools [07:19:26] Found java - /usr/local/bin/java [07:19:26] Found snpEff - /usr/local/bin/snpEff [07:19:26] Found samclip - /usr/local/bin/samclip [07:19:26] Found seqtk - /usr/local/bin/seqtk [07:19:26] Found parallel - /usr/local/bin/parallel [07:19:26] Found freebayes - /usr/local/bin/freebayes [07:19:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:19:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:19:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:19:26] Found vcfuniq - /usr/local/bin/vcfuniq [07:19:26] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:19:26] Found gzip - /bin/gzip [07:19:26] Found vt - /usr/local/bin/vt [07:19:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:19:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:19:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:19:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:19:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:19:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:19:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:19:27] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:48:42] This is snippy 4.6.0
Show full stderr[06:48:42] This is snippy 4.6.0 [06:48:42] Written by Torsten Seemann [06:48:42] Obtained from https://github.com/tseemann/snippy [06:48:42] Detected operating system: linux [06:48:42] Enabling bundled linux tools. [06:48:42] Found bwa - /usr/local/bin/bwa [06:48:42] Found bcftools - /usr/local/bin/bcftools [06:48:42] Found samtools - /usr/local/bin/samtools [06:48:42] Found java - /usr/local/bin/java [06:48:42] Found snpEff - /usr/local/bin/snpEff [06:48:42] Found samclip - /usr/local/bin/samclip [06:48:42] Found seqtk - /usr/local/bin/seqtk [06:48:42] Found parallel - /usr/local/bin/parallel [06:48:42] Found freebayes - /usr/local/bin/freebayes [06:48:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:48:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:48:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:48:42] Found vcfuniq - /usr/local/bin/vcfuniq [06:48:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:48:42] Found gzip - /bin/gzip [06:48:42] Found vt - /usr/local/bin/vt [06:48:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:48:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:48:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:48:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:48:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:48:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:48:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:48:43] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:48:51] This is snippy 4.6.0
Show full stderr[06:48:51] This is snippy 4.6.0 [06:48:51] Written by Torsten Seemann [06:48:51] Obtained from https://github.com/tseemann/snippy [06:48:51] Detected operating system: linux [06:48:51] Enabling bundled linux tools. [06:48:51] Found bwa - /usr/local/bin/bwa [06:48:51] Found bcftools - /usr/local/bin/bcftools [06:48:51] Found samtools - /usr/local/bin/samtools [06:48:51] Found java - /usr/local/bin/java [06:48:51] Found snpEff - /usr/local/bin/snpEff [06:48:51] Found samclip - /usr/local/bin/samclip [06:48:51] Found seqtk - /usr/local/bin/seqtk [06:48:51] Found parallel - /usr/local/bin/parallel [06:48:51] Found freebayes - /usr/local/bin/freebayes [06:48:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:48:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:48:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:48:51] Found vcfuniq - /usr/local/bin/vcfuniq [06:48:51] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:48:51] Found gzip - /bin/gzip [06:48:51] Found vt - /usr/local/bin/vt [06:48:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:48:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:48:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:48:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:48:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:48:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:48:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:48:52] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:32:11] This is snippy 4.6.0
Show full stderr[07:32:11] This is snippy 4.6.0 [07:32:11] Written by Torsten Seemann [07:32:11] Obtained from https://github.com/tseemann/snippy [07:32:11] Detected operating system: linux [07:32:11] Enabling bundled linux tools. [07:32:11] Found bwa - /usr/local/bin/bwa [07:32:11] Found bcftools - /usr/local/bin/bcftools [07:32:11] Found samtools - /usr/local/bin/samtools [07:32:11] Found java - /usr/local/bin/java [07:32:11] Found snpEff - /usr/local/bin/snpEff [07:32:11] Found samclip - /usr/local/bin/samclip [07:32:11] Found seqtk - /usr/local/bin/seqtk [07:32:11] Found parallel - /usr/local/bin/parallel [07:32:11] Found freebayes - /usr/local/bin/freebayes [07:32:11] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:32:11] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:32:11] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:32:11] Found vcfuniq - /usr/local/bin/vcfuniq [07:32:11] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:32:11] Found gzip - /bin/gzip [07:32:11] Found vt - /usr/local/bin/vt [07:32:11] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:32:11] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:32:11] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:32:11] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:32:11] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:32:12] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:32:12] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:32:12] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:32:58] This is snippy 4.6.0
Show full stderr[07:32:58] This is snippy 4.6.0 [07:32:58] Written by Torsten Seemann [07:32:58] Obtained from https://github.com/tseemann/snippy [07:32:58] Detected operating system: linux [07:32:58] Enabling bundled linux tools. [07:32:58] Found bwa - /usr/local/bin/bwa [07:32:58] Found bcftools - /usr/local/bin/bcftools [07:32:58] Found samtools - /usr/local/bin/samtools [07:32:58] Found java - /usr/local/bin/java [07:32:58] Found snpEff - /usr/local/bin/snpEff [07:32:58] Found samclip - /usr/local/bin/samclip [07:32:58] Found seqtk - /usr/local/bin/seqtk [07:32:58] Found parallel - /usr/local/bin/parallel [07:32:58] Found freebayes - /usr/local/bin/freebayes [07:32:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:32:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:32:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:32:58] Found vcfuniq - /usr/local/bin/vcfuniq [07:32:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:32:58] Found gzip - /bin/gzip [07:32:58] Found vt - /usr/local/bin/vt [07:32:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:32:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:32:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:32:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:32:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:32:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:32:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:32:59] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:49:19] This is snippy 4.6.0
Show full stderr[06:49:19] This is snippy 4.6.0 [06:49:19] Written by Torsten Seemann [06:49:19] Obtained from https://github.com/tseemann/snippy [06:49:19] Detected operating system: linux [06:49:19] Enabling bundled linux tools. [06:49:19] Found bwa - /usr/local/bin/bwa [06:49:19] Found bcftools - /usr/local/bin/bcftools [06:49:19] Found samtools - /usr/local/bin/samtools [06:49:19] Found java - /usr/local/bin/java [06:49:19] Found snpEff - /usr/local/bin/snpEff [06:49:19] Found samclip - /usr/local/bin/samclip [06:49:19] Found seqtk - /usr/local/bin/seqtk [06:49:19] Found parallel - /usr/local/bin/parallel [06:49:19] Found freebayes - /usr/local/bin/freebayes [06:49:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:49:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:49:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:49:19] Found vcfuniq - /usr/local/bin/vcfuniq [06:49:19] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:49:19] Found gzip - /bin/gzip [06:49:19] Found vt - /usr/local/bin/vt [06:49:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:49:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:49:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:49:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:49:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:49:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:49:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:49:20] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:38:29] This is snippy 4.6.0
Show full stderr[07:38:29] This is snippy 4.6.0 [07:38:29] Written by Torsten Seemann [07:38:29] Obtained from https://github.com/tseemann/snippy [07:38:29] Detected operating system: linux [07:38:29] Enabling bundled linux tools. [07:38:29] Found bwa - /usr/local/bin/bwa [07:38:29] Found bcftools - /usr/local/bin/bcftools [07:38:29] Found samtools - /usr/local/bin/samtools [07:38:29] Found java - /usr/local/bin/java [07:38:29] Found snpEff - /usr/local/bin/snpEff [07:38:29] Found samclip - /usr/local/bin/samclip [07:38:29] Found seqtk - /usr/local/bin/seqtk [07:38:29] Found parallel - /usr/local/bin/parallel [07:38:29] Found freebayes - /usr/local/bin/freebayes [07:38:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:38:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:38:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:38:29] Found vcfuniq - /usr/local/bin/vcfuniq [07:38:29] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:38:29] Found gzip - /bin/gzip [07:38:29] Found vt - /usr/local/bin/vt [07:38:29] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:38:29] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:38:29] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:38:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:38:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:38:30] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:38:30] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:38:30] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:50:35] This is snippy 4.6.0
Show full stderr[06:50:35] This is snippy 4.6.0 [06:50:35] Written by Torsten Seemann [06:50:35] Obtained from https://github.com/tseemann/snippy [06:50:35] Detected operating system: linux [06:50:35] Enabling bundled linux tools. [06:50:35] Found bwa - /usr/local/bin/bwa [06:50:35] Found bcftools - /usr/local/bin/bcftools [06:50:35] Found samtools - /usr/local/bin/samtools [06:50:35] Found java - /usr/local/bin/java [06:50:35] Found snpEff - /usr/local/bin/snpEff [06:50:35] Found samclip - /usr/local/bin/samclip [06:50:35] Found seqtk - /usr/local/bin/seqtk [06:50:35] Found parallel - /usr/local/bin/parallel [06:50:35] Found freebayes - /usr/local/bin/freebayes [06:50:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:50:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:50:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:50:35] Found vcfuniq - /usr/local/bin/vcfuniq [06:50:35] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:50:35] Found gzip - /bin/gzip [06:50:35] Found vt - /usr/local/bin/vt [06:50:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:50:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:50:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:50:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:50:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:50:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:50:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:50:36] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:45:02] This is snippy 4.6.0
Show full stderr[07:45:02] This is snippy 4.6.0 [07:45:02] Written by Torsten Seemann [07:45:02] Obtained from https://github.com/tseemann/snippy [07:45:02] Detected operating system: linux [07:45:02] Enabling bundled linux tools. [07:45:02] Found bwa - /usr/local/bin/bwa [07:45:02] Found bcftools - /usr/local/bin/bcftools [07:45:03] Found samtools - /usr/local/bin/samtools [07:45:03] Found java - /usr/local/bin/java [07:45:03] Found snpEff - /usr/local/bin/snpEff [07:45:03] Found samclip - /usr/local/bin/samclip [07:45:03] Found seqtk - /usr/local/bin/seqtk [07:45:03] Found parallel - /usr/local/bin/parallel [07:45:03] Found freebayes - /usr/local/bin/freebayes [07:45:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:45:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:45:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:45:03] Found vcfuniq - /usr/local/bin/vcfuniq [07:45:03] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:45:03] Found gzip - /bin/gzip [07:45:03] Found vt - /usr/local/bin/vt [07:45:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:45:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:45:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:45:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:45:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:45:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:45:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:45:03] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:50:47] This is snippy 4.6.0
Show full stderr[06:50:47] This is snippy 4.6.0 [06:50:47] Written by Torsten Seemann [06:50:47] Obtained from https://github.com/tseemann/snippy [06:50:47] Detected operating system: linux [06:50:47] Enabling bundled linux tools. [06:50:47] Found bwa - /usr/local/bin/bwa [06:50:47] Found bcftools - /usr/local/bin/bcftools [06:50:47] Found samtools - /usr/local/bin/samtools [06:50:47] Found java - /usr/local/bin/java [06:50:47] Found snpEff - /usr/local/bin/snpEff [06:50:47] Found samclip - /usr/local/bin/samclip [06:50:47] Found seqtk - /usr/local/bin/seqtk [06:50:47] Found parallel - /usr/local/bin/parallel [06:50:47] Found freebayes - /usr/local/bin/freebayes [06:50:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:50:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:50:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:50:47] Found vcfuniq - /usr/local/bin/vcfuniq [06:50:47] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:50:47] Found gzip - /bin/gzip [06:50:47] Found vt - /usr/local/bin/vt [06:50:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:50:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:50:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:50:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:50:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:50:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:50:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:50:48] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:50:50] This is snippy 4.6.0
Show full stderr[06:50:50] This is snippy 4.6.0 [06:50:50] Written by Torsten Seemann [06:50:50] Obtained from https://github.com/tseemann/snippy [06:50:50] Detected operating system: linux [06:50:50] Enabling bundled linux tools. [06:50:50] Found bwa - /usr/local/bin/bwa [06:50:50] Found bcftools - /usr/local/bin/bcftools [06:50:50] Found samtools - /usr/local/bin/samtools [06:50:50] Found java - /usr/local/bin/java [06:50:50] Found snpEff - /usr/local/bin/snpEff [06:50:50] Found samclip - /usr/local/bin/samclip [06:50:50] Found seqtk - /usr/local/bin/seqtk [06:50:50] Found parallel - /usr/local/bin/parallel [06:50:50] Found freebayes - /usr/local/bin/freebayes [06:50:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:50:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:50:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:50:50] Found vcfuniq - /usr/local/bin/vcfuniq [06:50:50] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:50:50] Found gzip - /bin/gzip [06:50:50] Found vt - /usr/local/bin/vt [06:50:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:50:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:50:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:50:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:50:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:50:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:50:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:50:51] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:50:57] This is snippy 4.6.0
Show full stderr[07:50:57] This is snippy 4.6.0 [07:50:57] Written by Torsten Seemann [07:50:57] Obtained from https://github.com/tseemann/snippy [07:50:57] Detected operating system: linux [07:50:57] Enabling bundled linux tools. [07:50:57] Found bwa - /usr/local/bin/bwa [07:50:57] Found bcftools - /usr/local/bin/bcftools [07:50:57] Found samtools - /usr/local/bin/samtools [07:50:57] Found java - /usr/local/bin/java [07:50:57] Found snpEff - /usr/local/bin/snpEff [07:50:57] Found samclip - /usr/local/bin/samclip [07:50:57] Found seqtk - /usr/local/bin/seqtk [07:50:57] Found parallel - /usr/local/bin/parallel [07:50:57] Found freebayes - /usr/local/bin/freebayes [07:50:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:50:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:50:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:50:57] Found vcfuniq - /usr/local/bin/vcfuniq [07:50:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:50:58] Found gzip - /bin/gzip [07:50:58] Found vt - /usr/local/bin/vt [07:50:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:50:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:50:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:50:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:50:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:50:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:50:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:50:58] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:57:02] This is snippy 4.6.0
Show full stderr[07:57:02] This is snippy 4.6.0 [07:57:02] Written by Torsten Seemann [07:57:02] Obtained from https://github.com/tseemann/snippy [07:57:02] Detected operating system: linux [07:57:02] Enabling bundled linux tools. [07:57:02] Found bwa - /usr/local/bin/bwa [07:57:02] Found bcftools - /usr/local/bin/bcftools [07:57:02] Found samtools - /usr/local/bin/samtools [07:57:02] Found java - /usr/local/bin/java [07:57:02] Found snpEff - /usr/local/bin/snpEff [07:57:02] Found samclip - /usr/local/bin/samclip [07:57:02] Found seqtk - /usr/local/bin/seqtk [07:57:02] Found parallel - /usr/local/bin/parallel [07:57:02] Found freebayes - /usr/local/bin/freebayes [07:57:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:57:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:57:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:57:02] Found vcfuniq - /usr/local/bin/vcfuniq [07:57:02] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:57:02] Found gzip - /bin/gzip [07:57:02] Found vt - /usr/local/bin/vt [07:57:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:57:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:57:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:57:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:57:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:57:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:57:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:57:02] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:57:04] This is snippy 4.6.0
Show full stderr[07:57:04] This is snippy 4.6.0 [07:57:04] Written by Torsten Seemann [07:57:04] Obtained from https://github.com/tseemann/snippy [07:57:04] Detected operating system: linux [07:57:04] Enabling bundled linux tools. [07:57:04] Found bwa - /usr/local/bin/bwa [07:57:04] Found bcftools - /usr/local/bin/bcftools [07:57:04] Found samtools - /usr/local/bin/samtools [07:57:04] Found java - /usr/local/bin/java [07:57:04] Found snpEff - /usr/local/bin/snpEff [07:57:04] Found samclip - /usr/local/bin/samclip [07:57:04] Found seqtk - /usr/local/bin/seqtk [07:57:04] Found parallel - /usr/local/bin/parallel [07:57:04] Found freebayes - /usr/local/bin/freebayes [07:57:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:57:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:57:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:57:04] Found vcfuniq - /usr/local/bin/vcfuniq [07:57:04] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:57:04] Found gzip - /bin/gzip [07:57:04] Found vt - /usr/local/bin/vt [07:57:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:57:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:57:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:57:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:57:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:57:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:57:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:57:05] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:12:56] This is snippy 4.6.0
Show full stderr[07:12:56] This is snippy 4.6.0 [07:12:56] Written by Torsten Seemann [07:12:56] Obtained from https://github.com/tseemann/snippy [07:12:56] Detected operating system: linux [07:12:56] Enabling bundled linux tools. [07:12:56] Found bwa - /usr/local/bin/bwa [07:12:56] Found bcftools - /usr/local/bin/bcftools [07:12:56] Found samtools - /usr/local/bin/samtools [07:12:56] Found java - /usr/local/bin/java [07:12:56] Found snpEff - /usr/local/bin/snpEff [07:12:56] Found samclip - /usr/local/bin/samclip [07:12:56] Found seqtk - /usr/local/bin/seqtk [07:12:56] Found parallel - /usr/local/bin/parallel [07:12:56] Found freebayes - /usr/local/bin/freebayes [07:12:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:12:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:12:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:12:56] Found vcfuniq - /usr/local/bin/vcfuniq [07:12:56] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:12:56] Found gzip - /bin/gzip [07:12:56] Found vt - /usr/local/bin/vt [07:12:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:12:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:12:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:12:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:12:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:12:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:12:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:12:57] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:13:32] This is snippy 4.6.0
Show full stderr[07:13:32] This is snippy 4.6.0 [07:13:32] Written by Torsten Seemann [07:13:32] Obtained from https://github.com/tseemann/snippy [07:13:32] Detected operating system: linux [07:13:32] Enabling bundled linux tools. [07:13:32] Found bwa - /usr/local/bin/bwa [07:13:32] Found bcftools - /usr/local/bin/bcftools [07:13:32] Found samtools - /usr/local/bin/samtools [07:13:32] Found java - /usr/local/bin/java [07:13:32] Found snpEff - /usr/local/bin/snpEff [07:13:32] Found samclip - /usr/local/bin/samclip [07:13:32] Found seqtk - /usr/local/bin/seqtk [07:13:32] Found parallel - /usr/local/bin/parallel [07:13:32] Found freebayes - /usr/local/bin/freebayes [07:13:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:13:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:13:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:13:32] Found vcfuniq - /usr/local/bin/vcfuniq [07:13:32] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:13:32] Found gzip - /bin/gzip [07:13:32] Found vt - /usr/local/bin/vt [07:13:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:13:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:13:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:13:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:13:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:13:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:13:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:13:33] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:18:50] This is snippy 4.6.0
Show full stderr[07:18:50] This is snippy 4.6.0 [07:18:50] Written by Torsten Seemann [07:18:50] Obtained from https://github.com/tseemann/snippy [07:18:50] Detected operating system: linux [07:18:50] Enabling bundled linux tools. [07:18:50] Found bwa - /usr/local/bin/bwa [07:18:50] Found bcftools - /usr/local/bin/bcftools [07:18:50] Found samtools - /usr/local/bin/samtools [07:18:50] Found java - /usr/local/bin/java [07:18:50] Found snpEff - /usr/local/bin/snpEff [07:18:50] Found samclip - /usr/local/bin/samclip [07:18:50] Found seqtk - /usr/local/bin/seqtk [07:18:50] Found parallel - /usr/local/bin/parallel [07:18:50] Found freebayes - /usr/local/bin/freebayes [07:18:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:18:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:18:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:18:50] Found vcfuniq - /usr/local/bin/vcfuniq [07:18:50] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:18:50] Found gzip - /bin/gzip [07:18:50] Found vt - /usr/local/bin/vt [07:18:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:18:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:18:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:18:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:18:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:18:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:18:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:18:51] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:52:14] This is snippy 4.6.0
Show full stderr[06:52:14] This is snippy 4.6.0 [06:52:14] Written by Torsten Seemann [06:52:14] Obtained from https://github.com/tseemann/snippy [06:52:14] Detected operating system: linux [06:52:14] Enabling bundled linux tools. [06:52:14] Found bwa - /usr/local/bin/bwa [06:52:14] Found bcftools - /usr/local/bin/bcftools [06:52:14] Found samtools - /usr/local/bin/samtools [06:52:14] Found java - /usr/local/bin/java [06:52:14] Found snpEff - /usr/local/bin/snpEff [06:52:14] Found samclip - /usr/local/bin/samclip [06:52:14] Found seqtk - /usr/local/bin/seqtk [06:52:14] Found parallel - /usr/local/bin/parallel [06:52:14] Found freebayes - /usr/local/bin/freebayes [06:52:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:52:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:52:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:52:14] Found vcfuniq - /usr/local/bin/vcfuniq [06:52:14] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:52:14] Found gzip - /bin/gzip [06:52:14] Found vt - /usr/local/bin/vt [06:52:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:52:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:52:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:52:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:52:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:52:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:52:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:52:15] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:45:31] This is snippy 4.6.0
Show full stderr[07:45:31] This is snippy 4.6.0 [07:45:31] Written by Torsten Seemann [07:45:31] Obtained from https://github.com/tseemann/snippy [07:45:31] Detected operating system: linux [07:45:31] Enabling bundled linux tools. [07:45:31] Found bwa - /usr/local/bin/bwa [07:45:31] Found bcftools - /usr/local/bin/bcftools [07:45:31] Found samtools - /usr/local/bin/samtools [07:45:31] Found java - /usr/local/bin/java [07:45:31] Found snpEff - /usr/local/bin/snpEff [07:45:31] Found samclip - /usr/local/bin/samclip [07:45:31] Found seqtk - /usr/local/bin/seqtk [07:45:31] Found parallel - /usr/local/bin/parallel [07:45:31] Found freebayes - /usr/local/bin/freebayes [07:45:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:45:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:45:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:45:31] Found vcfuniq - /usr/local/bin/vcfuniq [07:45:31] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:45:31] Found gzip - /bin/gzip [07:45:31] Found vt - /usr/local/bin/vt [07:45:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:45:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:45:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:45:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:45:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:45:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:45:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:45:32] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:49:54] This is snippy 4.6.0
Show full stderr[06:49:54] This is snippy 4.6.0 [06:49:54] Written by Torsten Seemann [06:49:54] Obtained from https://github.com/tseemann/snippy [06:49:54] Detected operating system: linux [06:49:54] Enabling bundled linux tools. [06:49:54] Found bwa - /usr/local/bin/bwa [06:49:54] Found bcftools - /usr/local/bin/bcftools [06:49:54] Found samtools - /usr/local/bin/samtools [06:49:54] Found java - /usr/local/bin/java [06:49:54] Found snpEff - /usr/local/bin/snpEff [06:49:54] Found samclip - /usr/local/bin/samclip [06:49:54] Found seqtk - /usr/local/bin/seqtk [06:49:54] Found parallel - /usr/local/bin/parallel [06:49:54] Found freebayes - /usr/local/bin/freebayes [06:49:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:49:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:49:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:49:54] Found vcfuniq - /usr/local/bin/vcfuniq [06:49:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:49:54] Found gzip - /bin/gzip [06:49:54] Found vt - /usr/local/bin/vt [06:49:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:49:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:49:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:49:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:49:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:49:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:49:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:49:55] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:50:07] This is snippy 4.6.0
Show full stderr[06:50:07] This is snippy 4.6.0 [06:50:07] Written by Torsten Seemann [06:50:07] Obtained from https://github.com/tseemann/snippy [06:50:07] Detected operating system: linux [06:50:07] Enabling bundled linux tools. [06:50:07] Found bwa - /usr/local/bin/bwa [06:50:07] Found bcftools - /usr/local/bin/bcftools [06:50:07] Found samtools - /usr/local/bin/samtools [06:50:07] Found java - /usr/local/bin/java [06:50:07] Found snpEff - /usr/local/bin/snpEff [06:50:07] Found samclip - /usr/local/bin/samclip [06:50:07] Found seqtk - /usr/local/bin/seqtk [06:50:07] Found parallel - /usr/local/bin/parallel [06:50:07] Found freebayes - /usr/local/bin/freebayes [06:50:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:50:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:50:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:50:07] Found vcfuniq - /usr/local/bin/vcfuniq [06:50:07] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:50:07] Found gzip - /bin/gzip [06:50:07] Found vt - /usr/local/bin/vt [06:50:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:50:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:50:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:50:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:50:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:50:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:50:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:50:08] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:12:59] This is snippy 4.6.0
Show full stderr[07:12:59] This is snippy 4.6.0 [07:12:59] Written by Torsten Seemann [07:12:59] Obtained from https://github.com/tseemann/snippy [07:12:59] Detected operating system: linux [07:12:59] Enabling bundled linux tools. [07:12:59] Found bwa - /usr/local/bin/bwa [07:12:59] Found bcftools - /usr/local/bin/bcftools [07:12:59] Found samtools - /usr/local/bin/samtools [07:12:59] Found java - /usr/local/bin/java [07:12:59] Found snpEff - /usr/local/bin/snpEff [07:12:59] Found samclip - /usr/local/bin/samclip [07:12:59] Found seqtk - /usr/local/bin/seqtk [07:12:59] Found parallel - /usr/local/bin/parallel [07:12:59] Found freebayes - /usr/local/bin/freebayes [07:12:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:12:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:12:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:12:59] Found vcfuniq - /usr/local/bin/vcfuniq [07:12:59] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:12:59] Found gzip - /bin/gzip [07:12:59] Found vt - /usr/local/bin/vt [07:12:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:12:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:13:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:13:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:13:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:13:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:13:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:13:07] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:25:47] This is snippy 4.6.0
Show full stderr[07:25:47] This is snippy 4.6.0 [07:25:47] Written by Torsten Seemann [07:25:47] Obtained from https://github.com/tseemann/snippy [07:25:47] Detected operating system: linux [07:25:47] Enabling bundled linux tools. [07:25:47] Found bwa - /usr/local/bin/bwa [07:25:47] Found bcftools - /usr/local/bin/bcftools [07:25:47] Found samtools - /usr/local/bin/samtools [07:25:47] Found java - /usr/local/bin/java [07:25:47] Found snpEff - /usr/local/bin/snpEff [07:25:47] Found samclip - /usr/local/bin/samclip [07:25:47] Found seqtk - /usr/local/bin/seqtk [07:25:47] Found parallel - /usr/local/bin/parallel [07:25:47] Found freebayes - /usr/local/bin/freebayes [07:25:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:25:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:25:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:25:47] Found vcfuniq - /usr/local/bin/vcfuniq [07:25:47] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:25:47] Found gzip - /bin/gzip [07:25:47] Found vt - /usr/local/bin/vt [07:25:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:25:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:25:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:25:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:25:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:25:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:25:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:25:48] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:26:02] This is snippy 4.6.0
Show full stderr[07:26:02] This is snippy 4.6.0 [07:26:02] Written by Torsten Seemann [07:26:02] Obtained from https://github.com/tseemann/snippy [07:26:02] Detected operating system: linux [07:26:02] Enabling bundled linux tools. [07:26:03] Found bwa - /usr/local/bin/bwa [07:26:03] Found bcftools - /usr/local/bin/bcftools [07:26:03] Found samtools - /usr/local/bin/samtools [07:26:03] Found java - /usr/local/bin/java [07:26:03] Found snpEff - /usr/local/bin/snpEff [07:26:03] Found samclip - /usr/local/bin/samclip [07:26:03] Found seqtk - /usr/local/bin/seqtk [07:26:03] Found parallel - /usr/local/bin/parallel [07:26:03] Found freebayes - /usr/local/bin/freebayes [07:26:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:26:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:26:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:26:03] Found vcfuniq - /usr/local/bin/vcfuniq [07:26:03] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:26:03] Found gzip - /bin/gzip [07:26:03] Found vt - /usr/local/bin/vt [07:26:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:26:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:26:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:26:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:26:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:26:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:26:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:26:03] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:26:44] This is snippy 4.6.0
Show full stderr[07:26:44] This is snippy 4.6.0 [07:26:44] Written by Torsten Seemann [07:26:44] Obtained from https://github.com/tseemann/snippy [07:26:44] Detected operating system: linux [07:26:44] Enabling bundled linux tools. [07:26:44] Found bwa - /usr/local/bin/bwa [07:26:44] Found bcftools - /usr/local/bin/bcftools [07:26:44] Found samtools - /usr/local/bin/samtools [07:26:44] Found java - /usr/local/bin/java [07:26:44] Found snpEff - /usr/local/bin/snpEff [07:26:44] Found samclip - /usr/local/bin/samclip [07:26:44] Found seqtk - /usr/local/bin/seqtk [07:26:44] Found parallel - /usr/local/bin/parallel [07:26:44] Found freebayes - /usr/local/bin/freebayes [07:26:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:26:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:26:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:26:45] Found vcfuniq - /usr/local/bin/vcfuniq [07:26:45] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:26:45] Found gzip - /bin/gzip [07:26:45] Found vt - /usr/local/bin/vt [07:26:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:26:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:26:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:26:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:26:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:26:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:26:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:26:45] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:51:01] This is snippy 4.6.0
Show full stderr[06:51:01] This is snippy 4.6.0 [06:51:01] Written by Torsten Seemann [06:51:01] Obtained from https://github.com/tseemann/snippy [06:51:01] Detected operating system: linux [06:51:01] Enabling bundled linux tools. [06:51:01] Found bwa - /usr/local/bin/bwa [06:51:01] Found bcftools - /usr/local/bin/bcftools [06:51:01] Found samtools - /usr/local/bin/samtools [06:51:01] Found java - /usr/local/bin/java [06:51:01] Found snpEff - /usr/local/bin/snpEff [06:51:01] Found samclip - /usr/local/bin/samclip [06:51:01] Found seqtk - /usr/local/bin/seqtk [06:51:01] Found parallel - /usr/local/bin/parallel [06:51:01] Found freebayes - /usr/local/bin/freebayes [06:51:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:51:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:51:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:51:01] Found vcfuniq - /usr/local/bin/vcfuniq [06:51:01] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:51:01] Found gzip - /bin/gzip [06:51:01] Found vt - /usr/local/bin/vt [06:51:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:51:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:51:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:51:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:51:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:51:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:51:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:51:02] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:51:07] This is snippy 4.6.0
Show full stderr[06:51:07] This is snippy 4.6.0 [06:51:07] Written by Torsten Seemann [06:51:07] Obtained from https://github.com/tseemann/snippy [06:51:07] Detected operating system: linux [06:51:07] Enabling bundled linux tools. [06:51:07] Found bwa - /usr/local/bin/bwa [06:51:07] Found bcftools - /usr/local/bin/bcftools [06:51:07] Found samtools - /usr/local/bin/samtools [06:51:07] Found java - /usr/local/bin/java [06:51:07] Found snpEff - /usr/local/bin/snpEff [06:51:07] Found samclip - /usr/local/bin/samclip [06:51:07] Found seqtk - /usr/local/bin/seqtk [06:51:07] Found parallel - /usr/local/bin/parallel [06:51:07] Found freebayes - /usr/local/bin/freebayes [06:51:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:51:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:51:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:51:07] Found vcfuniq - /usr/local/bin/vcfuniq [06:51:07] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:51:07] Found gzip - /bin/gzip [06:51:07] Found vt - /usr/local/bin/vt [06:51:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:51:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:51:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:51:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:51:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:51:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:51:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:51:08] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:51:16] This is snippy 4.6.0
Show full stderr[06:51:16] This is snippy 4.6.0 [06:51:16] Written by Torsten Seemann [06:51:16] Obtained from https://github.com/tseemann/snippy [06:51:16] Detected operating system: linux [06:51:16] Enabling bundled linux tools. [06:51:16] Found bwa - /usr/local/bin/bwa [06:51:16] Found bcftools - /usr/local/bin/bcftools [06:51:16] Found samtools - /usr/local/bin/samtools [06:51:16] Found java - /usr/local/bin/java [06:51:16] Found snpEff - /usr/local/bin/snpEff [06:51:16] Found samclip - /usr/local/bin/samclip [06:51:16] Found seqtk - /usr/local/bin/seqtk [06:51:16] Found parallel - /usr/local/bin/parallel [06:51:16] Found freebayes - /usr/local/bin/freebayes [06:51:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:51:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:51:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:51:16] Found vcfuniq - /usr/local/bin/vcfuniq [06:51:16] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:51:16] Found gzip - /bin/gzip [06:51:16] Found vt - /usr/local/bin/vt [06:51:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:51:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:51:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:51:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:51:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:51:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:51:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:51:17] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:52:42] This is snippy 4.6.0
Show full stderr[06:52:42] This is snippy 4.6.0 [06:52:42] Written by Torsten Seemann [06:52:42] Obtained from https://github.com/tseemann/snippy [06:52:42] Detected operating system: linux [06:52:42] Enabling bundled linux tools. [06:52:42] Found bwa - /usr/local/bin/bwa [06:52:42] Found bcftools - /usr/local/bin/bcftools [06:52:42] Found samtools - /usr/local/bin/samtools [06:52:42] Found java - /usr/local/bin/java [06:52:42] Found snpEff - /usr/local/bin/snpEff [06:52:42] Found samclip - /usr/local/bin/samclip [06:52:42] Found seqtk - /usr/local/bin/seqtk [06:52:42] Found parallel - /usr/local/bin/parallel [06:52:42] Found freebayes - /usr/local/bin/freebayes [06:52:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:52:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:52:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:52:42] Found vcfuniq - /usr/local/bin/vcfuniq [06:52:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:52:42] Found gzip - /bin/gzip [06:52:42] Found vt - /usr/local/bin/vt [06:52:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:52:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:52:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:52:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:52:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:52:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:52:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:52:43] Please supply a reference FASTA/GBK/EMBL file with --reference
1[08:15:36] This is snippy 4.6.0
Show full stderr[08:15:36] This is snippy 4.6.0 [08:15:36] Written by Torsten Seemann [08:15:36] Obtained from https://github.com/tseemann/snippy [08:15:36] Detected operating system: linux [08:15:36] Enabling bundled linux tools. [08:15:36] Found bwa - /usr/local/bin/bwa [08:15:36] Found bcftools - /usr/local/bin/bcftools [08:15:36] Found samtools - /usr/local/bin/samtools [08:15:36] Found java - /usr/local/bin/java [08:15:36] Found snpEff - /usr/local/bin/snpEff [08:15:36] Found samclip - /usr/local/bin/samclip [08:15:36] Found seqtk - /usr/local/bin/seqtk [08:15:37] Found parallel - /usr/local/bin/parallel [08:15:37] Found freebayes - /usr/local/bin/freebayes [08:15:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:15:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:15:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:15:37] Found vcfuniq - /usr/local/bin/vcfuniq [08:15:37] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:15:37] Found gzip - /bin/gzip [08:15:37] Found vt - /usr/local/bin/vt [08:15:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:15:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:15:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:15:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:15:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:15:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:15:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:15:37] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:53:21] This is snippy 4.6.0
Show full stderr[06:53:21] This is snippy 4.6.0 [06:53:21] Written by Torsten Seemann [06:53:21] Obtained from https://github.com/tseemann/snippy [06:53:21] Detected operating system: linux [06:53:21] Enabling bundled linux tools. [06:53:21] Found bwa - /usr/local/bin/bwa [06:53:21] Found bcftools - /usr/local/bin/bcftools [06:53:21] Found samtools - /usr/local/bin/samtools [06:53:21] Found java - /usr/local/bin/java [06:53:21] Found snpEff - /usr/local/bin/snpEff [06:53:21] Found samclip - /usr/local/bin/samclip [06:53:21] Found seqtk - /usr/local/bin/seqtk [06:53:21] Found parallel - /usr/local/bin/parallel [06:53:21] Found freebayes - /usr/local/bin/freebayes [06:53:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:53:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:53:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:53:21] Found vcfuniq - /usr/local/bin/vcfuniq [06:53:21] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:53:21] Found gzip - /bin/gzip [06:53:21] Found vt - /usr/local/bin/vt [06:53:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:53:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:53:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:53:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:53:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:53:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:53:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:53:22] Please supply a reference FASTA/GBK/EMBL file with --reference
1[08:16:29] This is snippy 4.6.0
Show full stderr[08:16:29] This is snippy 4.6.0 [08:16:29] Written by Torsten Seemann [08:16:29] Obtained from https://github.com/tseemann/snippy [08:16:29] Detected operating system: linux [08:16:29] Enabling bundled linux tools. [08:16:29] Found bwa - /usr/local/bin/bwa [08:16:29] Found bcftools - /usr/local/bin/bcftools [08:16:29] Found samtools - /usr/local/bin/samtools [08:16:29] Found java - /usr/local/bin/java [08:16:29] Found snpEff - /usr/local/bin/snpEff [08:16:29] Found samclip - /usr/local/bin/samclip [08:16:29] Found seqtk - /usr/local/bin/seqtk [08:16:29] Found parallel - /usr/local/bin/parallel [08:16:29] Found freebayes - /usr/local/bin/freebayes [08:16:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:16:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:16:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:16:29] Found vcfuniq - /usr/local/bin/vcfuniq [08:16:29] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:16:29] Found gzip - /bin/gzip [08:16:29] Found vt - /usr/local/bin/vt [08:16:29] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:16:29] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:16:29] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:16:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:16:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:16:30] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:16:30] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:16:30] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:54:40] This is snippy 4.6.0
Show full stderr[06:54:40] This is snippy 4.6.0 [06:54:40] Written by Torsten Seemann [06:54:40] Obtained from https://github.com/tseemann/snippy [06:54:40] Detected operating system: linux [06:54:40] Enabling bundled linux tools. [06:54:40] Found bwa - /usr/local/bin/bwa [06:54:40] Found bcftools - /usr/local/bin/bcftools [06:54:40] Found samtools - /usr/local/bin/samtools [06:54:40] Found java - /usr/local/bin/java [06:54:40] Found snpEff - /usr/local/bin/snpEff [06:54:40] Found samclip - /usr/local/bin/samclip [06:54:40] Found seqtk - /usr/local/bin/seqtk [06:54:40] Found parallel - /usr/local/bin/parallel [06:54:40] Found freebayes - /usr/local/bin/freebayes [06:54:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:54:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:54:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:54:40] Found vcfuniq - /usr/local/bin/vcfuniq [06:54:40] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:54:40] Found gzip - /bin/gzip [06:54:40] Found vt - /usr/local/bin/vt [06:54:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:54:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:54:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:54:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:54:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:54:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:54:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:54:41] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:50:22] This is snippy 4.6.0
Show full stderr[06:50:22] This is snippy 4.6.0 [06:50:22] Written by Torsten Seemann [06:50:22] Obtained from https://github.com/tseemann/snippy [06:50:22] Detected operating system: linux [06:50:22] Enabling bundled linux tools. [06:50:22] Found bwa - /usr/local/bin/bwa [06:50:22] Found bcftools - /usr/local/bin/bcftools [06:50:22] Found samtools - /usr/local/bin/samtools [06:50:22] Found java - /usr/local/bin/java [06:50:22] Found snpEff - /usr/local/bin/snpEff [06:50:22] Found samclip - /usr/local/bin/samclip [06:50:22] Found seqtk - /usr/local/bin/seqtk [06:50:22] Found parallel - /usr/local/bin/parallel [06:50:22] Found freebayes - /usr/local/bin/freebayes [06:50:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:50:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:50:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:50:22] Found vcfuniq - /usr/local/bin/vcfuniq [06:50:22] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:50:22] Found gzip - /bin/gzip [06:50:22] Found vt - /usr/local/bin/vt [06:50:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:50:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:50:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:50:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:50:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:50:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:50:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:50:23] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:51:46] This is snippy 4.6.0
Show full stderr[06:51:46] This is snippy 4.6.0 [06:51:46] Written by Torsten Seemann [06:51:46] Obtained from https://github.com/tseemann/snippy [06:51:46] Detected operating system: linux [06:51:46] Enabling bundled linux tools. [06:51:46] Found bwa - /usr/local/bin/bwa [06:51:46] Found bcftools - /usr/local/bin/bcftools [06:51:46] Found samtools - /usr/local/bin/samtools [06:51:46] Found java - /usr/local/bin/java [06:51:46] Found snpEff - /usr/local/bin/snpEff [06:51:46] Found samclip - /usr/local/bin/samclip [06:51:46] Found seqtk - /usr/local/bin/seqtk [06:51:46] Found parallel - /usr/local/bin/parallel [06:51:46] Found freebayes - /usr/local/bin/freebayes [06:51:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:51:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:51:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:51:46] Found vcfuniq - /usr/local/bin/vcfuniq [06:51:46] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:51:46] Found gzip - /bin/gzip [06:51:46] Found vt - /usr/local/bin/vt [06:51:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:51:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:51:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:51:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:51:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:51:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:51:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:51:47] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:52:28] This is snippy 4.6.0
Show full stderr[06:52:28] This is snippy 4.6.0 [06:52:28] Written by Torsten Seemann [06:52:28] Obtained from https://github.com/tseemann/snippy [06:52:28] Detected operating system: linux [06:52:28] Enabling bundled linux tools. [06:52:28] Found bwa - /usr/local/bin/bwa [06:52:28] Found bcftools - /usr/local/bin/bcftools [06:52:28] Found samtools - /usr/local/bin/samtools [06:52:28] Found java - /usr/local/bin/java [06:52:28] Found snpEff - /usr/local/bin/snpEff [06:52:28] Found samclip - /usr/local/bin/samclip [06:52:28] Found seqtk - /usr/local/bin/seqtk [06:52:28] Found parallel - /usr/local/bin/parallel [06:52:28] Found freebayes - /usr/local/bin/freebayes [06:52:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:52:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:52:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:52:28] Found vcfuniq - /usr/local/bin/vcfuniq [06:52:28] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:52:28] Found gzip - /bin/gzip [06:52:28] Found vt - /usr/local/bin/vt [06:52:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:52:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:52:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:52:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:52:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:52:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:52:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:52:29] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:53:03] This is snippy 4.6.0
Show full stderr[06:53:03] This is snippy 4.6.0 [06:53:03] Written by Torsten Seemann [06:53:03] Obtained from https://github.com/tseemann/snippy [06:53:03] Detected operating system: linux [06:53:03] Enabling bundled linux tools. [06:53:03] Found bwa - /usr/local/bin/bwa [06:53:03] Found bcftools - /usr/local/bin/bcftools [06:53:03] Found samtools - /usr/local/bin/samtools [06:53:03] Found java - /usr/local/bin/java [06:53:03] Found snpEff - /usr/local/bin/snpEff [06:53:03] Found samclip - /usr/local/bin/samclip [06:53:03] Found seqtk - /usr/local/bin/seqtk [06:53:03] Found parallel - /usr/local/bin/parallel [06:53:03] Found freebayes - /usr/local/bin/freebayes [06:53:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:53:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:53:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:53:03] Found vcfuniq - /usr/local/bin/vcfuniq [06:53:03] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:53:03] Found gzip - /bin/gzip [06:53:03] Found vt - /usr/local/bin/vt [06:53:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:53:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:53:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:53:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:53:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:53:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:53:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:53:04] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:53:24] This is snippy 4.6.0
Show full stderr[06:53:24] This is snippy 4.6.0 [06:53:24] Written by Torsten Seemann [06:53:24] Obtained from https://github.com/tseemann/snippy [06:53:24] Detected operating system: linux [06:53:24] Enabling bundled linux tools. [06:53:24] Found bwa - /usr/local/bin/bwa [06:53:24] Found bcftools - /usr/local/bin/bcftools [06:53:24] Found samtools - /usr/local/bin/samtools [06:53:24] Found java - /usr/local/bin/java [06:53:24] Found snpEff - /usr/local/bin/snpEff [06:53:24] Found samclip - /usr/local/bin/samclip [06:53:24] Found seqtk - /usr/local/bin/seqtk [06:53:24] Found parallel - /usr/local/bin/parallel [06:53:24] Found freebayes - /usr/local/bin/freebayes [06:53:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:53:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:53:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:53:24] Found vcfuniq - /usr/local/bin/vcfuniq [06:53:24] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:53:24] Found gzip - /bin/gzip [06:53:24] Found vt - /usr/local/bin/vt [06:53:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:53:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:53:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:53:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:53:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:53:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:53:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:53:25] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:51:19] This is snippy 4.6.0
Show full stderr[06:51:19] This is snippy 4.6.0 [06:51:19] Written by Torsten Seemann [06:51:19] Obtained from https://github.com/tseemann/snippy [06:51:19] Detected operating system: linux [06:51:19] Enabling bundled linux tools. [06:51:19] Found bwa - /usr/local/bin/bwa [06:51:19] Found bcftools - /usr/local/bin/bcftools [06:51:19] Found samtools - /usr/local/bin/samtools [06:51:19] Found java - /usr/local/bin/java [06:51:19] Found snpEff - /usr/local/bin/snpEff [06:51:19] Found samclip - /usr/local/bin/samclip [06:51:19] Found seqtk - /usr/local/bin/seqtk [06:51:19] Found parallel - /usr/local/bin/parallel [06:51:19] Found freebayes - /usr/local/bin/freebayes [06:51:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:51:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:51:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:51:19] Found vcfuniq - /usr/local/bin/vcfuniq [06:51:19] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:51:19] Found gzip - /bin/gzip [06:51:19] Found vt - /usr/local/bin/vt [06:51:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:51:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:51:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:51:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:51:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:51:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:51:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:51:20] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:51:34] This is snippy 4.6.0
Show full stderr[06:51:34] This is snippy 4.6.0 [06:51:34] Written by Torsten Seemann [06:51:34] Obtained from https://github.com/tseemann/snippy [06:51:34] Detected operating system: linux [06:51:34] Enabling bundled linux tools. [06:51:34] Found bwa - /usr/local/bin/bwa [06:51:34] Found bcftools - /usr/local/bin/bcftools [06:51:34] Found samtools - /usr/local/bin/samtools [06:51:34] Found java - /usr/local/bin/java [06:51:34] Found snpEff - /usr/local/bin/snpEff [06:51:34] Found samclip - /usr/local/bin/samclip [06:51:34] Found seqtk - /usr/local/bin/seqtk [06:51:34] Found parallel - /usr/local/bin/parallel [06:51:34] Found freebayes - /usr/local/bin/freebayes [06:51:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:51:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:51:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:51:34] Found vcfuniq - /usr/local/bin/vcfuniq [06:51:34] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:51:34] Found gzip - /bin/gzip [06:51:34] Found vt - /usr/local/bin/vt [06:51:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:51:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:51:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:51:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:51:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:51:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:51:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:51:35] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:52:01] This is snippy 4.6.0
Show full stderr[06:52:01] This is snippy 4.6.0 [06:52:01] Written by Torsten Seemann [06:52:01] Obtained from https://github.com/tseemann/snippy [06:52:01] Detected operating system: linux [06:52:01] Enabling bundled linux tools. [06:52:01] Found bwa - /usr/local/bin/bwa [06:52:01] Found bcftools - /usr/local/bin/bcftools [06:52:01] Found samtools - /usr/local/bin/samtools [06:52:01] Found java - /usr/local/bin/java [06:52:01] Found snpEff - /usr/local/bin/snpEff [06:52:01] Found samclip - /usr/local/bin/samclip [06:52:01] Found seqtk - /usr/local/bin/seqtk [06:52:01] Found parallel - /usr/local/bin/parallel [06:52:01] Found freebayes - /usr/local/bin/freebayes [06:52:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:52:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:52:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:52:01] Found vcfuniq - /usr/local/bin/vcfuniq [06:52:01] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:52:01] Found gzip - /bin/gzip [06:52:01] Found vt - /usr/local/bin/vt [06:52:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:52:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:52:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:52:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:52:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:52:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:52:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:52:02] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:52:25] This is snippy 4.6.0
Show full stderr[06:52:25] This is snippy 4.6.0 [06:52:25] Written by Torsten Seemann [06:52:25] Obtained from https://github.com/tseemann/snippy [06:52:25] Detected operating system: linux [06:52:25] Enabling bundled linux tools. [06:52:25] Found bwa - /usr/local/bin/bwa [06:52:25] Found bcftools - /usr/local/bin/bcftools [06:52:25] Found samtools - /usr/local/bin/samtools [06:52:25] Found java - /usr/local/bin/java [06:52:25] Found snpEff - /usr/local/bin/snpEff [06:52:25] Found samclip - /usr/local/bin/samclip [06:52:25] Found seqtk - /usr/local/bin/seqtk [06:52:25] Found parallel - /usr/local/bin/parallel [06:52:25] Found freebayes - /usr/local/bin/freebayes [06:52:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:52:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:52:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:52:25] Found vcfuniq - /usr/local/bin/vcfuniq [06:52:25] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:52:25] Found gzip - /bin/gzip [06:52:25] Found vt - /usr/local/bin/vt [06:52:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:52:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:52:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:52:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:52:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:52:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:52:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:52:26] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:52:39] This is snippy 4.6.0
Show full stderr[06:52:39] This is snippy 4.6.0 [06:52:39] Written by Torsten Seemann [06:52:39] Obtained from https://github.com/tseemann/snippy [06:52:39] Detected operating system: linux [06:52:39] Enabling bundled linux tools. [06:52:39] Found bwa - /usr/local/bin/bwa [06:52:39] Found bcftools - /usr/local/bin/bcftools [06:52:39] Found samtools - /usr/local/bin/samtools [06:52:39] Found java - /usr/local/bin/java [06:52:39] Found snpEff - /usr/local/bin/snpEff [06:52:39] Found samclip - /usr/local/bin/samclip [06:52:39] Found seqtk - /usr/local/bin/seqtk [06:52:39] Found parallel - /usr/local/bin/parallel [06:52:39] Found freebayes - /usr/local/bin/freebayes [06:52:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:52:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:52:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:52:39] Found vcfuniq - /usr/local/bin/vcfuniq [06:52:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:52:39] Found gzip - /bin/gzip [06:52:39] Found vt - /usr/local/bin/vt [06:52:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:52:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:52:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:52:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:52:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:52:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:52:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:52:40] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:52:54] This is snippy 4.6.0
Show full stderr[06:52:54] This is snippy 4.6.0 [06:52:54] Written by Torsten Seemann [06:52:54] Obtained from https://github.com/tseemann/snippy [06:52:54] Detected operating system: linux [06:52:54] Enabling bundled linux tools. [06:52:54] Found bwa - /usr/local/bin/bwa [06:52:54] Found bcftools - /usr/local/bin/bcftools [06:52:54] Found samtools - /usr/local/bin/samtools [06:52:54] Found java - /usr/local/bin/java [06:52:54] Found snpEff - /usr/local/bin/snpEff [06:52:54] Found samclip - /usr/local/bin/samclip [06:52:54] Found seqtk - /usr/local/bin/seqtk [06:52:54] Found parallel - /usr/local/bin/parallel [06:52:54] Found freebayes - /usr/local/bin/freebayes [06:52:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:52:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:52:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:52:54] Found vcfuniq - /usr/local/bin/vcfuniq [06:52:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:52:54] Found gzip - /bin/gzip [06:52:54] Found vt - /usr/local/bin/vt [06:52:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:52:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:52:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:52:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:52:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:52:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:52:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:52:55] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:52:57] This is snippy 4.6.0
Show full stderr[06:52:57] This is snippy 4.6.0 [06:52:57] Written by Torsten Seemann [06:52:57] Obtained from https://github.com/tseemann/snippy [06:52:57] Detected operating system: linux [06:52:57] Enabling bundled linux tools. [06:52:57] Found bwa - /usr/local/bin/bwa [06:52:57] Found bcftools - /usr/local/bin/bcftools [06:52:57] Found samtools - /usr/local/bin/samtools [06:52:57] Found java - /usr/local/bin/java [06:52:57] Found snpEff - /usr/local/bin/snpEff [06:52:57] Found samclip - /usr/local/bin/samclip [06:52:57] Found seqtk - /usr/local/bin/seqtk [06:52:57] Found parallel - /usr/local/bin/parallel [06:52:57] Found freebayes - /usr/local/bin/freebayes [06:52:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:52:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:52:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:52:57] Found vcfuniq - /usr/local/bin/vcfuniq [06:52:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:52:57] Found gzip - /bin/gzip [06:52:57] Found vt - /usr/local/bin/vt [06:52:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:52:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:52:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:52:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:52:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:52:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:52:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:52:58] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:53:04] This is snippy 4.6.0
Show full stderr[06:53:04] This is snippy 4.6.0 [06:53:04] Written by Torsten Seemann [06:53:04] Obtained from https://github.com/tseemann/snippy [06:53:04] Detected operating system: linux [06:53:04] Enabling bundled linux tools. [06:53:04] Found bwa - /usr/local/bin/bwa [06:53:04] Found bcftools - /usr/local/bin/bcftools [06:53:04] Found samtools - /usr/local/bin/samtools [06:53:04] Found java - /usr/local/bin/java [06:53:04] Found snpEff - /usr/local/bin/snpEff [06:53:04] Found samclip - /usr/local/bin/samclip [06:53:04] Found seqtk - /usr/local/bin/seqtk [06:53:04] Found parallel - /usr/local/bin/parallel [06:53:04] Found freebayes - /usr/local/bin/freebayes [06:53:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:53:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:53:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:53:04] Found vcfuniq - /usr/local/bin/vcfuniq [06:53:04] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:53:04] Found gzip - /bin/gzip [06:53:04] Found vt - /usr/local/bin/vt [06:53:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:53:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:53:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:53:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:53:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:53:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:53:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:53:05] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:53:07] This is snippy 4.6.0
Show full stderr[06:53:07] This is snippy 4.6.0 [06:53:07] Written by Torsten Seemann [06:53:07] Obtained from https://github.com/tseemann/snippy [06:53:07] Detected operating system: linux [06:53:07] Enabling bundled linux tools. [06:53:07] Found bwa - /usr/local/bin/bwa [06:53:07] Found bcftools - /usr/local/bin/bcftools [06:53:07] Found samtools - /usr/local/bin/samtools [06:53:07] Found java - /usr/local/bin/java [06:53:07] Found snpEff - /usr/local/bin/snpEff [06:53:07] Found samclip - /usr/local/bin/samclip [06:53:07] Found seqtk - /usr/local/bin/seqtk [06:53:07] Found parallel - /usr/local/bin/parallel [06:53:07] Found freebayes - /usr/local/bin/freebayes [06:53:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:53:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:53:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:53:07] Found vcfuniq - /usr/local/bin/vcfuniq [06:53:07] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:53:07] Found gzip - /bin/gzip [06:53:07] Found vt - /usr/local/bin/vt [06:53:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:53:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:53:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:53:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:53:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:53:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:53:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:53:08] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:53:10] This is snippy 4.6.0
Show full stderr[06:53:10] This is snippy 4.6.0 [06:53:10] Written by Torsten Seemann [06:53:10] Obtained from https://github.com/tseemann/snippy [06:53:10] Detected operating system: linux [06:53:10] Enabling bundled linux tools. [06:53:10] Found bwa - /usr/local/bin/bwa [06:53:10] Found bcftools - /usr/local/bin/bcftools [06:53:10] Found samtools - /usr/local/bin/samtools [06:53:10] Found java - /usr/local/bin/java [06:53:10] Found snpEff - /usr/local/bin/snpEff [06:53:10] Found samclip - /usr/local/bin/samclip [06:53:10] Found seqtk - /usr/local/bin/seqtk [06:53:10] Found parallel - /usr/local/bin/parallel [06:53:10] Found freebayes - /usr/local/bin/freebayes [06:53:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:53:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:53:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:53:10] Found vcfuniq - /usr/local/bin/vcfuniq [06:53:10] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:53:10] Found gzip - /bin/gzip [06:53:10] Found vt - /usr/local/bin/vt [06:53:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:53:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:53:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:53:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:53:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:53:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:53:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:53:11] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:54:13] This is snippy 4.6.0
Show full stderr[06:54:13] This is snippy 4.6.0 [06:54:13] Written by Torsten Seemann [06:54:13] Obtained from https://github.com/tseemann/snippy [06:54:13] Detected operating system: linux [06:54:13] Enabling bundled linux tools. [06:54:13] Found bwa - /usr/local/bin/bwa [06:54:13] Found bcftools - /usr/local/bin/bcftools [06:54:13] Found samtools - /usr/local/bin/samtools [06:54:13] Found java - /usr/local/bin/java [06:54:13] Found snpEff - /usr/local/bin/snpEff [06:54:13] Found samclip - /usr/local/bin/samclip [06:54:13] Found seqtk - /usr/local/bin/seqtk [06:54:13] Found parallel - /usr/local/bin/parallel [06:54:13] Found freebayes - /usr/local/bin/freebayes [06:54:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:54:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:54:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:54:13] Found vcfuniq - /usr/local/bin/vcfuniq [06:54:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:54:13] Found gzip - /bin/gzip [06:54:13] Found vt - /usr/local/bin/vt [06:54:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:54:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:54:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:54:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:54:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:54:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:54:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:54:14] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:50:49] This is snippy 4.6.0
Show full stderr[07:50:49] This is snippy 4.6.0 [07:50:49] Written by Torsten Seemann [07:50:49] Obtained from https://github.com/tseemann/snippy [07:50:49] Detected operating system: linux [07:50:49] Enabling bundled linux tools. [07:50:49] Found bwa - /usr/local/bin/bwa [07:50:49] Found bcftools - /usr/local/bin/bcftools [07:50:49] Found samtools - /usr/local/bin/samtools [07:50:49] Found java - /usr/local/bin/java [07:50:49] Found snpEff - /usr/local/bin/snpEff [07:50:49] Found samclip - /usr/local/bin/samclip [07:50:49] Found seqtk - /usr/local/bin/seqtk [07:50:49] Found parallel - /usr/local/bin/parallel [07:50:49] Found freebayes - /usr/local/bin/freebayes [07:50:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:50:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:50:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:50:49] Found vcfuniq - /usr/local/bin/vcfuniq [07:50:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:50:49] Found gzip - /bin/gzip [07:50:49] Found vt - /usr/local/bin/vt [07:50:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:50:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:50:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:50:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:50:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:50:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:50:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:50:50] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:56:01] This is snippy 4.6.0
Show full stderr[06:56:01] This is snippy 4.6.0 [06:56:01] Written by Torsten Seemann [06:56:01] Obtained from https://github.com/tseemann/snippy [06:56:01] Detected operating system: linux [06:56:01] Enabling bundled linux tools. [06:56:01] Found bwa - /usr/local/bin/bwa [06:56:01] Found bcftools - /usr/local/bin/bcftools [06:56:01] Found samtools - /usr/local/bin/samtools [06:56:01] Found java - /usr/local/bin/java [06:56:01] Found snpEff - /usr/local/bin/snpEff [06:56:01] Found samclip - /usr/local/bin/samclip [06:56:01] Found seqtk - /usr/local/bin/seqtk [06:56:01] Found parallel - /usr/local/bin/parallel [06:56:01] Found freebayes - /usr/local/bin/freebayes [06:56:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:56:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:56:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:56:01] Found vcfuniq - /usr/local/bin/vcfuniq [06:56:01] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:56:01] Found gzip - /bin/gzip [06:56:01] Found vt - /usr/local/bin/vt [06:56:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:56:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:56:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:56:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:56:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:56:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:56:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:56:02] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:58:00] This is snippy 4.6.0
Show full stderr[06:58:00] This is snippy 4.6.0 [06:58:00] Written by Torsten Seemann [06:58:00] Obtained from https://github.com/tseemann/snippy [06:58:00] Detected operating system: linux [06:58:00] Enabling bundled linux tools. [06:58:00] Found bwa - /usr/local/bin/bwa [06:58:00] Found bcftools - /usr/local/bin/bcftools [06:58:00] Found samtools - /usr/local/bin/samtools [06:58:00] Found java - /usr/local/bin/java [06:58:00] Found snpEff - /usr/local/bin/snpEff [06:58:00] Found samclip - /usr/local/bin/samclip [06:58:00] Found seqtk - /usr/local/bin/seqtk [06:58:00] Found parallel - /usr/local/bin/parallel [06:58:00] Found freebayes - /usr/local/bin/freebayes [06:58:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:58:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:58:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:58:00] Found vcfuniq - /usr/local/bin/vcfuniq [06:58:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:58:00] Found gzip - /bin/gzip [06:58:00] Found vt - /usr/local/bin/vt [06:58:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:58:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:58:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:58:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:58:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:58:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:58:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:58:01] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:58:14] This is snippy 4.6.0
Show full stderr[06:58:14] This is snippy 4.6.0 [06:58:14] Written by Torsten Seemann [06:58:14] Obtained from https://github.com/tseemann/snippy [06:58:14] Detected operating system: linux [06:58:14] Enabling bundled linux tools. [06:58:14] Found bwa - /usr/local/bin/bwa [06:58:14] Found bcftools - /usr/local/bin/bcftools [06:58:14] Found samtools - /usr/local/bin/samtools [06:58:14] Found java - /usr/local/bin/java [06:58:14] Found snpEff - /usr/local/bin/snpEff [06:58:14] Found samclip - /usr/local/bin/samclip [06:58:14] Found seqtk - /usr/local/bin/seqtk [06:58:14] Found parallel - /usr/local/bin/parallel [06:58:14] Found freebayes - /usr/local/bin/freebayes [06:58:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:58:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:58:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:58:14] Found vcfuniq - /usr/local/bin/vcfuniq [06:58:14] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:58:14] Found gzip - /bin/gzip [06:58:14] Found vt - /usr/local/bin/vt [06:58:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:58:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:58:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:58:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:58:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:58:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:58:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:58:15] Please supply a reference FASTA/GBK/EMBL file with --reference
1[08:21:38] This is snippy 4.6.0
Show full stderr[08:21:38] This is snippy 4.6.0 [08:21:38] Written by Torsten Seemann [08:21:38] Obtained from https://github.com/tseemann/snippy [08:21:38] Detected operating system: linux [08:21:38] Enabling bundled linux tools. [08:21:38] Found bwa - /usr/local/bin/bwa [08:21:38] Found bcftools - /usr/local/bin/bcftools [08:21:38] Found samtools - /usr/local/bin/samtools [08:21:38] Found java - /usr/local/bin/java [08:21:38] Found snpEff - /usr/local/bin/snpEff [08:21:38] Found samclip - /usr/local/bin/samclip [08:21:38] Found seqtk - /usr/local/bin/seqtk [08:21:38] Found parallel - /usr/local/bin/parallel [08:21:38] Found freebayes - /usr/local/bin/freebayes [08:21:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:21:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:21:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:21:38] Found vcfuniq - /usr/local/bin/vcfuniq [08:21:38] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:21:38] Found gzip - /bin/gzip [08:21:38] Found vt - /usr/local/bin/vt [08:21:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:21:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:21:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:21:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:21:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:21:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:21:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:21:38] Please supply a reference FASTA/GBK/EMBL file with --reference
1[08:22:39] This is snippy 4.6.0
Show full stderr[08:22:39] This is snippy 4.6.0 [08:22:39] Written by Torsten Seemann [08:22:39] Obtained from https://github.com/tseemann/snippy [08:22:39] Detected operating system: linux [08:22:39] Enabling bundled linux tools. [08:22:39] Found bwa - /usr/local/bin/bwa [08:22:39] Found bcftools - /usr/local/bin/bcftools [08:22:39] Found samtools - /usr/local/bin/samtools [08:22:39] Found java - /usr/local/bin/java [08:22:39] Found snpEff - /usr/local/bin/snpEff [08:22:39] Found samclip - /usr/local/bin/samclip [08:22:39] Found seqtk - /usr/local/bin/seqtk [08:22:39] Found parallel - /usr/local/bin/parallel [08:22:39] Found freebayes - /usr/local/bin/freebayes [08:22:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:22:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:22:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:22:39] Found vcfuniq - /usr/local/bin/vcfuniq [08:22:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:22:39] Found gzip - /bin/gzip [08:22:39] Found vt - /usr/local/bin/vt [08:22:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:22:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:22:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:22:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:22:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:22:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:22:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:22:40] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:55:13] This is snippy 4.6.0
Show full stderr[06:55:13] This is snippy 4.6.0 [06:55:13] Written by Torsten Seemann [06:55:13] Obtained from https://github.com/tseemann/snippy [06:55:13] Detected operating system: linux [06:55:13] Enabling bundled linux tools. [06:55:13] Found bwa - /usr/local/bin/bwa [06:55:13] Found bcftools - /usr/local/bin/bcftools [06:55:13] Found samtools - /usr/local/bin/samtools [06:55:13] Found java - /usr/local/bin/java [06:55:13] Found snpEff - /usr/local/bin/snpEff [06:55:13] Found samclip - /usr/local/bin/samclip [06:55:13] Found seqtk - /usr/local/bin/seqtk [06:55:13] Found parallel - /usr/local/bin/parallel [06:55:13] Found freebayes - /usr/local/bin/freebayes [06:55:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:55:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:55:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:55:13] Found vcfuniq - /usr/local/bin/vcfuniq [06:55:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:55:13] Found gzip - /bin/gzip [06:55:13] Found vt - /usr/local/bin/vt [06:55:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:55:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:55:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:55:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:55:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:55:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:55:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:55:14] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:55:43] This is snippy 4.6.0
Show full stderr[06:55:43] This is snippy 4.6.0 [06:55:43] Written by Torsten Seemann [06:55:43] Obtained from https://github.com/tseemann/snippy [06:55:43] Detected operating system: linux [06:55:43] Enabling bundled linux tools. [06:55:43] Found bwa - /usr/local/bin/bwa [06:55:43] Found bcftools - /usr/local/bin/bcftools [06:55:43] Found samtools - /usr/local/bin/samtools [06:55:43] Found java - /usr/local/bin/java [06:55:43] Found snpEff - /usr/local/bin/snpEff [06:55:43] Found samclip - /usr/local/bin/samclip [06:55:43] Found seqtk - /usr/local/bin/seqtk [06:55:43] Found parallel - /usr/local/bin/parallel [06:55:43] Found freebayes - /usr/local/bin/freebayes [06:55:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:55:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:55:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:55:43] Found vcfuniq - /usr/local/bin/vcfuniq [06:55:43] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:55:43] Found gzip - /bin/gzip [06:55:43] Found vt - /usr/local/bin/vt [06:55:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:55:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:55:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:55:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:55:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:55:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:55:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:55:44] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:56:04] This is snippy 4.6.0
Show full stderr[06:56:04] This is snippy 4.6.0 [06:56:04] Written by Torsten Seemann [06:56:04] Obtained from https://github.com/tseemann/snippy [06:56:04] Detected operating system: linux [06:56:04] Enabling bundled linux tools. [06:56:04] Found bwa - /usr/local/bin/bwa [06:56:04] Found bcftools - /usr/local/bin/bcftools [06:56:04] Found samtools - /usr/local/bin/samtools [06:56:04] Found java - /usr/local/bin/java [06:56:04] Found snpEff - /usr/local/bin/snpEff [06:56:04] Found samclip - /usr/local/bin/samclip [06:56:04] Found seqtk - /usr/local/bin/seqtk [06:56:04] Found parallel - /usr/local/bin/parallel [06:56:04] Found freebayes - /usr/local/bin/freebayes [06:56:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:56:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:56:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:56:04] Found vcfuniq - /usr/local/bin/vcfuniq [06:56:04] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:56:04] Found gzip - /bin/gzip [06:56:04] Found vt - /usr/local/bin/vt [06:56:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:56:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:56:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:56:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:56:05] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:56:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:56:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:56:05] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:56:44] This is snippy 4.6.0
Show full stderr[06:56:44] This is snippy 4.6.0 [06:56:44] Written by Torsten Seemann [06:56:44] Obtained from https://github.com/tseemann/snippy [06:56:44] Detected operating system: linux [06:56:44] Enabling bundled linux tools. [06:56:44] Found bwa - /usr/local/bin/bwa [06:56:44] Found bcftools - /usr/local/bin/bcftools [06:56:44] Found samtools - /usr/local/bin/samtools [06:56:44] Found java - /usr/local/bin/java [06:56:44] Found snpEff - /usr/local/bin/snpEff [06:56:44] Found samclip - /usr/local/bin/samclip [06:56:44] Found seqtk - /usr/local/bin/seqtk [06:56:44] Found parallel - /usr/local/bin/parallel [06:56:44] Found freebayes - /usr/local/bin/freebayes [06:56:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:56:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:56:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:56:44] Found vcfuniq - /usr/local/bin/vcfuniq [06:56:44] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:56:44] Found gzip - /bin/gzip [06:56:44] Found vt - /usr/local/bin/vt [06:56:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:56:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:56:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:56:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:56:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:56:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:56:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:56:45] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:54:25] This is snippy 4.6.0
Show full stderr[06:54:25] This is snippy 4.6.0 [06:54:25] Written by Torsten Seemann [06:54:25] Obtained from https://github.com/tseemann/snippy [06:54:25] Detected operating system: linux [06:54:25] Enabling bundled linux tools. [06:54:25] Found bwa - /usr/local/bin/bwa [06:54:25] Found bcftools - /usr/local/bin/bcftools [06:54:25] Found samtools - /usr/local/bin/samtools [06:54:25] Found java - /usr/local/bin/java [06:54:25] Found snpEff - /usr/local/bin/snpEff [06:54:25] Found samclip - /usr/local/bin/samclip [06:54:25] Found seqtk - /usr/local/bin/seqtk [06:54:25] Found parallel - /usr/local/bin/parallel [06:54:25] Found freebayes - /usr/local/bin/freebayes [06:54:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:54:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:54:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:54:25] Found vcfuniq - /usr/local/bin/vcfuniq [06:54:25] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:54:25] Found gzip - /bin/gzip [06:54:25] Found vt - /usr/local/bin/vt [06:54:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:54:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:54:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:54:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:54:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:54:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:54:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:54:26] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:54:58] This is snippy 4.6.0
Show full stderr[06:54:58] This is snippy 4.6.0 [06:54:58] Written by Torsten Seemann [06:54:58] Obtained from https://github.com/tseemann/snippy [06:54:58] Detected operating system: linux [06:54:58] Enabling bundled linux tools. [06:54:58] Found bwa - /usr/local/bin/bwa [06:54:58] Found bcftools - /usr/local/bin/bcftools [06:54:58] Found samtools - /usr/local/bin/samtools [06:54:58] Found java - /usr/local/bin/java [06:54:58] Found snpEff - /usr/local/bin/snpEff [06:54:58] Found samclip - /usr/local/bin/samclip [06:54:58] Found seqtk - /usr/local/bin/seqtk [06:54:58] Found parallel - /usr/local/bin/parallel [06:54:58] Found freebayes - /usr/local/bin/freebayes [06:54:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:54:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:54:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:54:58] Found vcfuniq - /usr/local/bin/vcfuniq [06:54:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:54:58] Found gzip - /bin/gzip [06:54:58] Found vt - /usr/local/bin/vt [06:54:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:54:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:54:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:54:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:54:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:54:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:54:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:54:59] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:56:18] This is snippy 4.6.0
Show full stderr[06:56:18] This is snippy 4.6.0 [06:56:18] Written by Torsten Seemann [06:56:18] Obtained from https://github.com/tseemann/snippy [06:56:18] Detected operating system: linux [06:56:18] Enabling bundled linux tools. [06:56:18] Found bwa - /usr/local/bin/bwa [06:56:18] Found bcftools - /usr/local/bin/bcftools [06:56:18] Found samtools - /usr/local/bin/samtools [06:56:18] Found java - /usr/local/bin/java [06:56:18] Found snpEff - /usr/local/bin/snpEff [06:56:18] Found samclip - /usr/local/bin/samclip [06:56:18] Found seqtk - /usr/local/bin/seqtk [06:56:18] Found parallel - /usr/local/bin/parallel [06:56:18] Found freebayes - /usr/local/bin/freebayes [06:56:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:56:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:56:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:56:18] Found vcfuniq - /usr/local/bin/vcfuniq [06:56:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:56:18] Found gzip - /bin/gzip [06:56:18] Found vt - /usr/local/bin/vt [06:56:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:56:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:56:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:56:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:56:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:56:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:56:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:56:19] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:54:10] This is snippy 4.6.0
Show full stderr[06:54:10] This is snippy 4.6.0 [06:54:10] Written by Torsten Seemann [06:54:10] Obtained from https://github.com/tseemann/snippy [06:54:10] Detected operating system: linux [06:54:10] Enabling bundled linux tools. [06:54:10] Found bwa - /usr/local/bin/bwa [06:54:10] Found bcftools - /usr/local/bin/bcftools [06:54:10] Found samtools - /usr/local/bin/samtools [06:54:10] Found java - /usr/local/bin/java [06:54:10] Found snpEff - /usr/local/bin/snpEff [06:54:10] Found samclip - /usr/local/bin/samclip [06:54:10] Found seqtk - /usr/local/bin/seqtk [06:54:10] Found parallel - /usr/local/bin/parallel [06:54:10] Found freebayes - /usr/local/bin/freebayes [06:54:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:54:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:54:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:54:10] Found vcfuniq - /usr/local/bin/vcfuniq [06:54:10] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:54:10] Found gzip - /bin/gzip [06:54:10] Found vt - /usr/local/bin/vt [06:54:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:54:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:54:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:54:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:54:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:54:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:54:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:54:11] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:55:25] This is snippy 4.6.0
Show full stderr[06:55:25] This is snippy 4.6.0 [06:55:25] Written by Torsten Seemann [06:55:25] Obtained from https://github.com/tseemann/snippy [06:55:25] Detected operating system: linux [06:55:25] Enabling bundled linux tools. [06:55:25] Found bwa - /usr/local/bin/bwa [06:55:25] Found bcftools - /usr/local/bin/bcftools [06:55:25] Found samtools - /usr/local/bin/samtools [06:55:25] Found java - /usr/local/bin/java [06:55:25] Found snpEff - /usr/local/bin/snpEff [06:55:25] Found samclip - /usr/local/bin/samclip [06:55:25] Found seqtk - /usr/local/bin/seqtk [06:55:25] Found parallel - /usr/local/bin/parallel [06:55:25] Found freebayes - /usr/local/bin/freebayes [06:55:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:55:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:55:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:55:25] Found vcfuniq - /usr/local/bin/vcfuniq [06:55:25] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:55:25] Found gzip - /bin/gzip [06:55:25] Found vt - /usr/local/bin/vt [06:55:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:55:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:55:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:55:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:55:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:55:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:55:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:55:26] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:55:28] This is snippy 4.6.0
Show full stderr[06:55:28] This is snippy 4.6.0 [06:55:28] Written by Torsten Seemann [06:55:28] Obtained from https://github.com/tseemann/snippy [06:55:28] Detected operating system: linux [06:55:28] Enabling bundled linux tools. [06:55:28] Found bwa - /usr/local/bin/bwa [06:55:28] Found bcftools - /usr/local/bin/bcftools [06:55:28] Found samtools - /usr/local/bin/samtools [06:55:28] Found java - /usr/local/bin/java [06:55:28] Found snpEff - /usr/local/bin/snpEff [06:55:28] Found samclip - /usr/local/bin/samclip [06:55:28] Found seqtk - /usr/local/bin/seqtk [06:55:28] Found parallel - /usr/local/bin/parallel [06:55:28] Found freebayes - /usr/local/bin/freebayes [06:55:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:55:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:55:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:55:28] Found vcfuniq - /usr/local/bin/vcfuniq [06:55:28] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:55:28] Found gzip - /bin/gzip [06:55:28] Found vt - /usr/local/bin/vt [06:55:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:55:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:55:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:55:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:55:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:55:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:55:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:55:29] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:55:34] This is snippy 4.6.0
Show full stderr[06:55:34] This is snippy 4.6.0 [06:55:34] Written by Torsten Seemann [06:55:34] Obtained from https://github.com/tseemann/snippy [06:55:34] Detected operating system: linux [06:55:34] Enabling bundled linux tools. [06:55:34] Found bwa - /usr/local/bin/bwa [06:55:34] Found bcftools - /usr/local/bin/bcftools [06:55:34] Found samtools - /usr/local/bin/samtools [06:55:34] Found java - /usr/local/bin/java [06:55:34] Found snpEff - /usr/local/bin/snpEff [06:55:34] Found samclip - /usr/local/bin/samclip [06:55:34] Found seqtk - /usr/local/bin/seqtk [06:55:34] Found parallel - /usr/local/bin/parallel [06:55:34] Found freebayes - /usr/local/bin/freebayes [06:55:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:55:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:55:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:55:34] Found vcfuniq - /usr/local/bin/vcfuniq [06:55:34] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:55:34] Found gzip - /bin/gzip [06:55:34] Found vt - /usr/local/bin/vt [06:55:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:55:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:55:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:55:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:55:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:55:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:55:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:55:35] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:55:46] This is snippy 4.6.0
Show full stderr[06:55:46] This is snippy 4.6.0 [06:55:46] Written by Torsten Seemann [06:55:46] Obtained from https://github.com/tseemann/snippy [06:55:46] Detected operating system: linux [06:55:46] Enabling bundled linux tools. [06:55:46] Found bwa - /usr/local/bin/bwa [06:55:46] Found bcftools - /usr/local/bin/bcftools [06:55:46] Found samtools - /usr/local/bin/samtools [06:55:46] Found java - /usr/local/bin/java [06:55:46] Found snpEff - /usr/local/bin/snpEff [06:55:46] Found samclip - /usr/local/bin/samclip [06:55:46] Found seqtk - /usr/local/bin/seqtk [06:55:46] Found parallel - /usr/local/bin/parallel [06:55:46] Found freebayes - /usr/local/bin/freebayes [06:55:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:55:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:55:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:55:46] Found vcfuniq - /usr/local/bin/vcfuniq [06:55:46] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:55:46] Found gzip - /bin/gzip [06:55:46] Found vt - /usr/local/bin/vt [06:55:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:55:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:55:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:55:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:55:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:55:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:55:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:55:47] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:56:14] This is snippy 4.6.0
Show full stderr[06:56:14] This is snippy 4.6.0 [06:56:14] Written by Torsten Seemann [06:56:14] Obtained from https://github.com/tseemann/snippy [06:56:14] Detected operating system: linux [06:56:14] Enabling bundled linux tools. [06:56:14] Found bwa - /usr/local/bin/bwa [06:56:14] Found bcftools - /usr/local/bin/bcftools [06:56:14] Found samtools - /usr/local/bin/samtools [06:56:14] Found java - /usr/local/bin/java [06:56:14] Found snpEff - /usr/local/bin/snpEff [06:56:14] Found samclip - /usr/local/bin/samclip [06:56:14] Found seqtk - /usr/local/bin/seqtk [06:56:14] Found parallel - /usr/local/bin/parallel [06:56:14] Found freebayes - /usr/local/bin/freebayes [06:56:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:56:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:56:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:56:14] Found vcfuniq - /usr/local/bin/vcfuniq [06:56:14] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:56:14] Found gzip - /bin/gzip [06:56:14] Found vt - /usr/local/bin/vt [06:56:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:56:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:56:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:56:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:56:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:56:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:56:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:56:15] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:32:12] This is snippy 4.6.0
Show full stderr[07:32:12] This is snippy 4.6.0 [07:32:12] Written by Torsten Seemann [07:32:12] Obtained from https://github.com/tseemann/snippy [07:32:12] Detected operating system: linux [07:32:12] Enabling bundled linux tools. [07:32:12] Found bwa - /usr/local/bin/bwa [07:32:12] Found bcftools - /usr/local/bin/bcftools [07:32:12] Found samtools - /usr/local/bin/samtools [07:32:12] Found java - /usr/local/bin/java [07:32:12] Found snpEff - /usr/local/bin/snpEff [07:32:12] Found samclip - /usr/local/bin/samclip [07:32:12] Found seqtk - /usr/local/bin/seqtk [07:32:12] Found parallel - /usr/local/bin/parallel [07:32:12] Found freebayes - /usr/local/bin/freebayes [07:32:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:32:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:32:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:32:12] Found vcfuniq - /usr/local/bin/vcfuniq [07:32:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:32:12] Found gzip - /bin/gzip [07:32:12] Found vt - /usr/local/bin/vt [07:32:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:32:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:32:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:32:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:32:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:32:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:32:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:32:13] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:56:30] This is snippy 4.6.0
Show full stderr[06:56:30] This is snippy 4.6.0 [06:56:30] Written by Torsten Seemann [06:56:30] Obtained from https://github.com/tseemann/snippy [06:56:30] Detected operating system: linux [06:56:30] Enabling bundled linux tools. [06:56:30] Found bwa - /usr/local/bin/bwa [06:56:30] Found bcftools - /usr/local/bin/bcftools [06:56:30] Found samtools - /usr/local/bin/samtools [06:56:30] Found java - /usr/local/bin/java [06:56:30] Found snpEff - /usr/local/bin/snpEff [06:56:30] Found samclip - /usr/local/bin/samclip [06:56:30] Found seqtk - /usr/local/bin/seqtk [06:56:30] Found parallel - /usr/local/bin/parallel [06:56:30] Found freebayes - /usr/local/bin/freebayes [06:56:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:56:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:56:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:56:30] Found vcfuniq - /usr/local/bin/vcfuniq [06:56:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:56:30] Found gzip - /bin/gzip [06:56:30] Found vt - /usr/local/bin/vt [06:56:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:56:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:56:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:56:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:56:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:56:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:56:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:56:31] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:32:55] This is snippy 4.6.0
Show full stderr[07:32:55] This is snippy 4.6.0 [07:32:55] Written by Torsten Seemann [07:32:55] Obtained from https://github.com/tseemann/snippy [07:32:55] Detected operating system: linux [07:32:55] Enabling bundled linux tools. [07:32:55] Found bwa - /usr/local/bin/bwa [07:32:55] Found bcftools - /usr/local/bin/bcftools [07:32:55] Found samtools - /usr/local/bin/samtools [07:32:55] Found java - /usr/local/bin/java [07:32:55] Found snpEff - /usr/local/bin/snpEff [07:32:55] Found samclip - /usr/local/bin/samclip [07:32:55] Found seqtk - /usr/local/bin/seqtk [07:32:55] Found parallel - /usr/local/bin/parallel [07:32:55] Found freebayes - /usr/local/bin/freebayes [07:32:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:32:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:32:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:32:55] Found vcfuniq - /usr/local/bin/vcfuniq [07:32:55] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:32:55] Found gzip - /bin/gzip [07:32:55] Found vt - /usr/local/bin/vt [07:32:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:32:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:32:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:32:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:32:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:32:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:32:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:32:56] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:58:35] This is snippy 4.6.0
Show full stderr[06:58:35] This is snippy 4.6.0 [06:58:35] Written by Torsten Seemann [06:58:35] Obtained from https://github.com/tseemann/snippy [06:58:35] Detected operating system: linux [06:58:35] Enabling bundled linux tools. [06:58:35] Found bwa - /usr/local/bin/bwa [06:58:35] Found bcftools - /usr/local/bin/bcftools [06:58:35] Found samtools - /usr/local/bin/samtools [06:58:35] Found java - /usr/local/bin/java [06:58:35] Found snpEff - /usr/local/bin/snpEff [06:58:35] Found samclip - /usr/local/bin/samclip [06:58:35] Found seqtk - /usr/local/bin/seqtk [06:58:35] Found parallel - /usr/local/bin/parallel [06:58:35] Found freebayes - /usr/local/bin/freebayes [06:58:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:58:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:58:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:58:35] Found vcfuniq - /usr/local/bin/vcfuniq [06:58:35] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:58:35] Found gzip - /bin/gzip [06:58:35] Found vt - /usr/local/bin/vt [06:58:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:58:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:58:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:58:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:58:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:58:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:58:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:58:35] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:58:45] This is snippy 4.6.0
Show full stderr[06:58:45] This is snippy 4.6.0 [06:58:45] Written by Torsten Seemann [06:58:45] Obtained from https://github.com/tseemann/snippy [06:58:45] Detected operating system: linux [06:58:45] Enabling bundled linux tools. [06:58:45] Found bwa - /usr/local/bin/bwa [06:58:45] Found bcftools - /usr/local/bin/bcftools [06:58:45] Found samtools - /usr/local/bin/samtools [06:58:45] Found java - /usr/local/bin/java [06:58:45] Found snpEff - /usr/local/bin/snpEff [06:58:46] Found samclip - /usr/local/bin/samclip [06:58:46] Found seqtk - /usr/local/bin/seqtk [06:58:46] Found parallel - /usr/local/bin/parallel [06:58:46] Found freebayes - /usr/local/bin/freebayes [06:58:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:58:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:58:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:58:46] Found vcfuniq - /usr/local/bin/vcfuniq [06:58:46] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:58:46] Found gzip - /bin/gzip [06:58:46] Found vt - /usr/local/bin/vt [06:58:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:58:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:58:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:58:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:58:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:58:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:58:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:58:46] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:58:48] This is snippy 4.6.0
Show full stderr[06:58:48] This is snippy 4.6.0 [06:58:48] Written by Torsten Seemann [06:58:48] Obtained from https://github.com/tseemann/snippy [06:58:48] Detected operating system: linux [06:58:48] Enabling bundled linux tools. [06:58:48] Found bwa - /usr/local/bin/bwa [06:58:48] Found bcftools - /usr/local/bin/bcftools [06:58:48] Found samtools - /usr/local/bin/samtools [06:58:48] Found java - /usr/local/bin/java [06:58:48] Found snpEff - /usr/local/bin/snpEff [06:58:48] Found samclip - /usr/local/bin/samclip [06:58:49] Found seqtk - /usr/local/bin/seqtk [06:58:49] Found parallel - /usr/local/bin/parallel [06:58:49] Found freebayes - /usr/local/bin/freebayes [06:58:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:58:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:58:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:58:49] Found vcfuniq - /usr/local/bin/vcfuniq [06:58:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:58:49] Found gzip - /bin/gzip [06:58:49] Found vt - /usr/local/bin/vt [06:58:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:58:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:58:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:58:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:58:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:58:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:58:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:58:49] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:59:04] This is snippy 4.6.0
Show full stderr[06:59:04] This is snippy 4.6.0 [06:59:04] Written by Torsten Seemann [06:59:04] Obtained from https://github.com/tseemann/snippy [06:59:04] Detected operating system: linux [06:59:04] Enabling bundled linux tools. [06:59:04] Found bwa - /usr/local/bin/bwa [06:59:04] Found bcftools - /usr/local/bin/bcftools [06:59:04] Found samtools - /usr/local/bin/samtools [06:59:04] Found java - /usr/local/bin/java [06:59:04] Found snpEff - /usr/local/bin/snpEff [06:59:04] Found samclip - /usr/local/bin/samclip [06:59:04] Found seqtk - /usr/local/bin/seqtk [06:59:04] Found parallel - /usr/local/bin/parallel [06:59:04] Found freebayes - /usr/local/bin/freebayes [06:59:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:59:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:59:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:59:04] Found vcfuniq - /usr/local/bin/vcfuniq [06:59:04] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:59:04] Found gzip - /bin/gzip [06:59:04] Found vt - /usr/local/bin/vt [06:59:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:59:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:59:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:59:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:59:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:59:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:59:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:59:05] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:59:13] This is snippy 4.6.0
Show full stderr[06:59:13] This is snippy 4.6.0 [06:59:13] Written by Torsten Seemann [06:59:13] Obtained from https://github.com/tseemann/snippy [06:59:13] Detected operating system: linux [06:59:13] Enabling bundled linux tools. [06:59:13] Found bwa - /usr/local/bin/bwa [06:59:13] Found bcftools - /usr/local/bin/bcftools [06:59:13] Found samtools - /usr/local/bin/samtools [06:59:13] Found java - /usr/local/bin/java [06:59:13] Found snpEff - /usr/local/bin/snpEff [06:59:13] Found samclip - /usr/local/bin/samclip [06:59:13] Found seqtk - /usr/local/bin/seqtk [06:59:13] Found parallel - /usr/local/bin/parallel [06:59:13] Found freebayes - /usr/local/bin/freebayes [06:59:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:59:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:59:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:59:13] Found vcfuniq - /usr/local/bin/vcfuniq [06:59:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:59:13] Found gzip - /bin/gzip [06:59:13] Found vt - /usr/local/bin/vt [06:59:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:59:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:59:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:59:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:59:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:59:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:59:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:59:13] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:00:13] This is snippy 4.6.0
Show full stderr[07:00:13] This is snippy 4.6.0 [07:00:13] Written by Torsten Seemann [07:00:13] Obtained from https://github.com/tseemann/snippy [07:00:13] Detected operating system: linux [07:00:13] Enabling bundled linux tools. [07:00:13] Found bwa - /usr/local/bin/bwa [07:00:13] Found bcftools - /usr/local/bin/bcftools [07:00:13] Found samtools - /usr/local/bin/samtools [07:00:13] Found java - /usr/local/bin/java [07:00:13] Found snpEff - /usr/local/bin/snpEff [07:00:13] Found samclip - /usr/local/bin/samclip [07:00:13] Found seqtk - /usr/local/bin/seqtk [07:00:13] Found parallel - /usr/local/bin/parallel [07:00:13] Found freebayes - /usr/local/bin/freebayes [07:00:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:00:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:00:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:00:13] Found vcfuniq - /usr/local/bin/vcfuniq [07:00:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:00:13] Found gzip - /bin/gzip [07:00:13] Found vt - /usr/local/bin/vt [07:00:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:00:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:00:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:00:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:00:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:00:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:00:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:00:13] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:51:04] This is snippy 4.6.0
Show full stderr[07:51:04] This is snippy 4.6.0 [07:51:04] Written by Torsten Seemann [07:51:04] Obtained from https://github.com/tseemann/snippy [07:51:04] Detected operating system: linux [07:51:04] Enabling bundled linux tools. [07:51:04] Found bwa - /usr/local/bin/bwa [07:51:04] Found bcftools - /usr/local/bin/bcftools [07:51:04] Found samtools - /usr/local/bin/samtools [07:51:04] Found java - /usr/local/bin/java [07:51:04] Found snpEff - /usr/local/bin/snpEff [07:51:04] Found samclip - /usr/local/bin/samclip [07:51:04] Found seqtk - /usr/local/bin/seqtk [07:51:04] Found parallel - /usr/local/bin/parallel [07:51:04] Found freebayes - /usr/local/bin/freebayes [07:51:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:51:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:51:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:51:04] Found vcfuniq - /usr/local/bin/vcfuniq [07:51:04] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:51:04] Found gzip - /bin/gzip [07:51:04] Found vt - /usr/local/bin/vt [07:51:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:51:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:51:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:51:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:51:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:51:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:51:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:51:05] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:00:49] This is snippy 4.6.0
Show full stderr[07:00:49] This is snippy 4.6.0 [07:00:49] Written by Torsten Seemann [07:00:49] Obtained from https://github.com/tseemann/snippy [07:00:49] Detected operating system: linux [07:00:49] Enabling bundled linux tools. [07:00:49] Found bwa - /usr/local/bin/bwa [07:00:49] Found bcftools - /usr/local/bin/bcftools [07:00:49] Found samtools - /usr/local/bin/samtools [07:00:49] Found java - /usr/local/bin/java [07:00:49] Found snpEff - /usr/local/bin/snpEff [07:00:49] Found samclip - /usr/local/bin/samclip [07:00:49] Found seqtk - /usr/local/bin/seqtk [07:00:49] Found parallel - /usr/local/bin/parallel [07:00:49] Found freebayes - /usr/local/bin/freebayes [07:00:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:00:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:00:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:00:49] Found vcfuniq - /usr/local/bin/vcfuniq [07:00:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:00:49] Found gzip - /bin/gzip [07:00:49] Found vt - /usr/local/bin/vt [07:00:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:00:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:00:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:00:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:00:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:00:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:00:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:00:49] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:57:22] This is snippy 4.6.0
Show full stderr[07:57:22] This is snippy 4.6.0 [07:57:22] Written by Torsten Seemann [07:57:22] Obtained from https://github.com/tseemann/snippy [07:57:22] Detected operating system: linux [07:57:22] Enabling bundled linux tools. [07:57:22] Found bwa - /usr/local/bin/bwa [07:57:22] Found bcftools - /usr/local/bin/bcftools [07:57:22] Found samtools - /usr/local/bin/samtools [07:57:22] Found java - /usr/local/bin/java [07:57:22] Found snpEff - /usr/local/bin/snpEff [07:57:22] Found samclip - /usr/local/bin/samclip [07:57:22] Found seqtk - /usr/local/bin/seqtk [07:57:22] Found parallel - /usr/local/bin/parallel [07:57:22] Found freebayes - /usr/local/bin/freebayes [07:57:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:57:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:57:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:57:22] Found vcfuniq - /usr/local/bin/vcfuniq [07:57:22] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:57:22] Found gzip - /bin/gzip [07:57:22] Found vt - /usr/local/bin/vt [07:57:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:57:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:57:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:57:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:57:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:57:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:57:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:57:23] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:57:36] This is snippy 4.6.0
Show full stderr[06:57:36] This is snippy 4.6.0 [06:57:36] Written by Torsten Seemann [06:57:36] Obtained from https://github.com/tseemann/snippy [06:57:36] Detected operating system: linux [06:57:36] Enabling bundled linux tools. [06:57:36] Found bwa - /usr/local/bin/bwa [06:57:36] Found bcftools - /usr/local/bin/bcftools [06:57:36] Found samtools - /usr/local/bin/samtools [06:57:36] Found java - /usr/local/bin/java [06:57:36] Found snpEff - /usr/local/bin/snpEff [06:57:36] Found samclip - /usr/local/bin/samclip [06:57:36] Found seqtk - /usr/local/bin/seqtk [06:57:36] Found parallel - /usr/local/bin/parallel [06:57:36] Found freebayes - /usr/local/bin/freebayes [06:57:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:57:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:57:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:57:36] Found vcfuniq - /usr/local/bin/vcfuniq [06:57:36] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:57:36] Found gzip - /bin/gzip [06:57:36] Found vt - /usr/local/bin/vt [06:57:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:57:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:57:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:57:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:57:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:57:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:57:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:57:36] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:58:06] This is snippy 4.6.0
Show full stderr[06:58:06] This is snippy 4.6.0 [06:58:06] Written by Torsten Seemann [06:58:06] Obtained from https://github.com/tseemann/snippy [06:58:06] Detected operating system: linux [06:58:06] Enabling bundled linux tools. [06:58:06] Found bwa - /usr/local/bin/bwa [06:58:06] Found bcftools - /usr/local/bin/bcftools [06:58:06] Found samtools - /usr/local/bin/samtools [06:58:06] Found java - /usr/local/bin/java [06:58:06] Found snpEff - /usr/local/bin/snpEff [06:58:06] Found samclip - /usr/local/bin/samclip [06:58:06] Found seqtk - /usr/local/bin/seqtk [06:58:06] Found parallel - /usr/local/bin/parallel [06:58:06] Found freebayes - /usr/local/bin/freebayes [06:58:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:58:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:58:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:58:06] Found vcfuniq - /usr/local/bin/vcfuniq [06:58:06] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:58:06] Found gzip - /bin/gzip [06:58:06] Found vt - /usr/local/bin/vt [06:58:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:58:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:58:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:58:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:58:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:58:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:58:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:58:07] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:58:15] This is snippy 4.6.0
Show full stderr[06:58:15] This is snippy 4.6.0 [06:58:15] Written by Torsten Seemann [06:58:15] Obtained from https://github.com/tseemann/snippy [06:58:15] Detected operating system: linux [06:58:15] Enabling bundled linux tools. [06:58:15] Found bwa - /usr/local/bin/bwa [06:58:15] Found bcftools - /usr/local/bin/bcftools [06:58:15] Found samtools - /usr/local/bin/samtools [06:58:15] Found java - /usr/local/bin/java [06:58:15] Found snpEff - /usr/local/bin/snpEff [06:58:15] Found samclip - /usr/local/bin/samclip [06:58:15] Found seqtk - /usr/local/bin/seqtk [06:58:15] Found parallel - /usr/local/bin/parallel [06:58:15] Found freebayes - /usr/local/bin/freebayes [06:58:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:58:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:58:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:58:15] Found vcfuniq - /usr/local/bin/vcfuniq [06:58:16] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:58:16] Found gzip - /bin/gzip [06:58:16] Found vt - /usr/local/bin/vt [06:58:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:58:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:58:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:58:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:58:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:58:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:58:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:58:16] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:59:19] This is snippy 4.6.0
Show full stderr[06:59:19] This is snippy 4.6.0 [06:59:19] Written by Torsten Seemann [06:59:19] Obtained from https://github.com/tseemann/snippy [06:59:19] Detected operating system: linux [06:59:19] Enabling bundled linux tools. [06:59:19] Found bwa - /usr/local/bin/bwa [06:59:19] Found bcftools - /usr/local/bin/bcftools [06:59:19] Found samtools - /usr/local/bin/samtools [06:59:19] Found java - /usr/local/bin/java [06:59:19] Found snpEff - /usr/local/bin/snpEff [06:59:19] Found samclip - /usr/local/bin/samclip [06:59:19] Found seqtk - /usr/local/bin/seqtk [06:59:19] Found parallel - /usr/local/bin/parallel [06:59:19] Found freebayes - /usr/local/bin/freebayes [06:59:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:59:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:59:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:59:19] Found vcfuniq - /usr/local/bin/vcfuniq [06:59:19] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:59:19] Found gzip - /bin/gzip [06:59:19] Found vt - /usr/local/bin/vt [06:59:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:59:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:59:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:59:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:59:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:59:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:59:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:59:19] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:59:40] This is snippy 4.6.0
Show full stderr[06:59:40] This is snippy 4.6.0 [06:59:40] Written by Torsten Seemann [06:59:40] Obtained from https://github.com/tseemann/snippy [06:59:40] Detected operating system: linux [06:59:40] Enabling bundled linux tools. [06:59:40] Found bwa - /usr/local/bin/bwa [06:59:40] Found bcftools - /usr/local/bin/bcftools [06:59:40] Found samtools - /usr/local/bin/samtools [06:59:40] Found java - /usr/local/bin/java [06:59:40] Found snpEff - /usr/local/bin/snpEff [06:59:40] Found samclip - /usr/local/bin/samclip [06:59:40] Found seqtk - /usr/local/bin/seqtk [06:59:40] Found parallel - /usr/local/bin/parallel [06:59:40] Found freebayes - /usr/local/bin/freebayes [06:59:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:59:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:59:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:59:40] Found vcfuniq - /usr/local/bin/vcfuniq [06:59:40] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:59:40] Found gzip - /bin/gzip [06:59:40] Found vt - /usr/local/bin/vt [06:59:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:59:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:59:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:59:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:59:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:59:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:59:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:59:40] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:59:58] This is snippy 4.6.0
Show full stderr[06:59:58] This is snippy 4.6.0 [06:59:58] Written by Torsten Seemann [06:59:58] Obtained from https://github.com/tseemann/snippy [06:59:58] Detected operating system: linux [06:59:58] Enabling bundled linux tools. [06:59:58] Found bwa - /usr/local/bin/bwa [06:59:58] Found bcftools - /usr/local/bin/bcftools [06:59:58] Found samtools - /usr/local/bin/samtools [06:59:58] Found java - /usr/local/bin/java [06:59:58] Found snpEff - /usr/local/bin/snpEff [06:59:58] Found samclip - /usr/local/bin/samclip [06:59:58] Found seqtk - /usr/local/bin/seqtk [06:59:58] Found parallel - /usr/local/bin/parallel [06:59:58] Found freebayes - /usr/local/bin/freebayes [06:59:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:59:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:59:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:59:58] Found vcfuniq - /usr/local/bin/vcfuniq [06:59:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:59:58] Found gzip - /bin/gzip [06:59:58] Found vt - /usr/local/bin/vt [06:59:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:59:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:59:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:59:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:59:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:59:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:59:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:59:59] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:00:04] This is snippy 4.6.0
Show full stderr[07:00:04] This is snippy 4.6.0 [07:00:04] Written by Torsten Seemann [07:00:04] Obtained from https://github.com/tseemann/snippy [07:00:04] Detected operating system: linux [07:00:04] Enabling bundled linux tools. [07:00:04] Found bwa - /usr/local/bin/bwa [07:00:04] Found bcftools - /usr/local/bin/bcftools [07:00:04] Found samtools - /usr/local/bin/samtools [07:00:04] Found java - /usr/local/bin/java [07:00:04] Found snpEff - /usr/local/bin/snpEff [07:00:04] Found samclip - /usr/local/bin/samclip [07:00:04] Found seqtk - /usr/local/bin/seqtk [07:00:04] Found parallel - /usr/local/bin/parallel [07:00:04] Found freebayes - /usr/local/bin/freebayes [07:00:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:00:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:00:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:00:04] Found vcfuniq - /usr/local/bin/vcfuniq [07:00:04] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:00:04] Found gzip - /bin/gzip [07:00:04] Found vt - /usr/local/bin/vt [07:00:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:00:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:00:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:00:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:00:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:00:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:00:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:00:04] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:00:19] This is snippy 4.6.0
Show full stderr[07:00:19] This is snippy 4.6.0 [07:00:19] Written by Torsten Seemann [07:00:19] Obtained from https://github.com/tseemann/snippy [07:00:19] Detected operating system: linux [07:00:19] Enabling bundled linux tools. [07:00:19] Found bwa - /usr/local/bin/bwa [07:00:19] Found bcftools - /usr/local/bin/bcftools [07:00:19] Found samtools - /usr/local/bin/samtools [07:00:19] Found java - /usr/local/bin/java [07:00:19] Found snpEff - /usr/local/bin/snpEff [07:00:19] Found samclip - /usr/local/bin/samclip [07:00:19] Found seqtk - /usr/local/bin/seqtk [07:00:19] Found parallel - /usr/local/bin/parallel [07:00:19] Found freebayes - /usr/local/bin/freebayes [07:00:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:00:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:00:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:00:19] Found vcfuniq - /usr/local/bin/vcfuniq [07:00:19] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:00:19] Found gzip - /bin/gzip [07:00:19] Found vt - /usr/local/bin/vt [07:00:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:00:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:00:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:00:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:00:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:00:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:00:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:00:19] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:56:58] This is snippy 4.6.0
Show full stderr[06:56:58] This is snippy 4.6.0 [06:56:58] Written by Torsten Seemann [06:56:58] Obtained from https://github.com/tseemann/snippy [06:56:58] Detected operating system: linux [06:56:58] Enabling bundled linux tools. [06:56:58] Found bwa - /usr/local/bin/bwa [06:56:58] Found bcftools - /usr/local/bin/bcftools [06:56:58] Found samtools - /usr/local/bin/samtools [06:56:58] Found java - /usr/local/bin/java [06:56:58] Found snpEff - /usr/local/bin/snpEff [06:56:58] Found samclip - /usr/local/bin/samclip [06:56:58] Found seqtk - /usr/local/bin/seqtk [06:56:58] Found parallel - /usr/local/bin/parallel [06:56:58] Found freebayes - /usr/local/bin/freebayes [06:56:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:56:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:56:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:56:58] Found vcfuniq - /usr/local/bin/vcfuniq [06:56:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:56:58] Found gzip - /bin/gzip [06:56:58] Found vt - /usr/local/bin/vt [06:56:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:56:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:56:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:56:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:56:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:56:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:56:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:56:59] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:57:14] This is snippy 4.6.0
Show full stderr[06:57:14] This is snippy 4.6.0 [06:57:14] Written by Torsten Seemann [06:57:14] Obtained from https://github.com/tseemann/snippy [06:57:14] Detected operating system: linux [06:57:14] Enabling bundled linux tools. [06:57:14] Found bwa - /usr/local/bin/bwa [06:57:14] Found bcftools - /usr/local/bin/bcftools [06:57:14] Found samtools - /usr/local/bin/samtools [06:57:14] Found java - /usr/local/bin/java [06:57:14] Found snpEff - /usr/local/bin/snpEff [06:57:14] Found samclip - /usr/local/bin/samclip [06:57:14] Found seqtk - /usr/local/bin/seqtk [06:57:14] Found parallel - /usr/local/bin/parallel [06:57:14] Found freebayes - /usr/local/bin/freebayes [06:57:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:57:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:57:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:57:14] Found vcfuniq - /usr/local/bin/vcfuniq [06:57:14] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:57:14] Found gzip - /bin/gzip [06:57:14] Found vt - /usr/local/bin/vt [06:57:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:57:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:57:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:57:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:57:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:57:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:57:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:57:15] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:58:43] This is snippy 4.6.0
Show full stderr[06:58:43] This is snippy 4.6.0 [06:58:43] Written by Torsten Seemann [06:58:43] Obtained from https://github.com/tseemann/snippy [06:58:43] Detected operating system: linux [06:58:43] Enabling bundled linux tools. [06:58:43] Found bwa - /usr/local/bin/bwa [06:58:43] Found bcftools - /usr/local/bin/bcftools [06:58:43] Found samtools - /usr/local/bin/samtools [06:58:43] Found java - /usr/local/bin/java [06:58:43] Found snpEff - /usr/local/bin/snpEff [06:58:43] Found samclip - /usr/local/bin/samclip [06:58:43] Found seqtk - /usr/local/bin/seqtk [06:58:43] Found parallel - /usr/local/bin/parallel [06:58:43] Found freebayes - /usr/local/bin/freebayes [06:58:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:58:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:58:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:58:43] Found vcfuniq - /usr/local/bin/vcfuniq [06:58:43] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:58:43] Found gzip - /bin/gzip [06:58:43] Found vt - /usr/local/bin/vt [06:58:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:58:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:58:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:58:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:58:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:58:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:58:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:58:44] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:59:12] This is snippy 4.6.0
Show full stderr[06:59:12] This is snippy 4.6.0 [06:59:12] Written by Torsten Seemann [06:59:12] Obtained from https://github.com/tseemann/snippy [06:59:12] Detected operating system: linux [06:59:12] Enabling bundled linux tools. [06:59:13] Found bwa - /usr/local/bin/bwa [06:59:13] Found bcftools - /usr/local/bin/bcftools [06:59:13] Found samtools - /usr/local/bin/samtools [06:59:13] Found java - /usr/local/bin/java [06:59:13] Found snpEff - /usr/local/bin/snpEff [06:59:13] Found samclip - /usr/local/bin/samclip [06:59:13] Found seqtk - /usr/local/bin/seqtk [06:59:13] Found parallel - /usr/local/bin/parallel [06:59:13] Found freebayes - /usr/local/bin/freebayes [06:59:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:59:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:59:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:59:13] Found vcfuniq - /usr/local/bin/vcfuniq [06:59:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:59:13] Found gzip - /bin/gzip [06:59:13] Found vt - /usr/local/bin/vt [06:59:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:59:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:59:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:59:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:59:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:59:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:59:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:59:13] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:59:14] This is snippy 4.6.0
Show full stderr[06:59:14] This is snippy 4.6.0 [06:59:14] Written by Torsten Seemann [06:59:14] Obtained from https://github.com/tseemann/snippy [06:59:14] Detected operating system: linux [06:59:14] Enabling bundled linux tools. [06:59:14] Found bwa - /usr/local/bin/bwa [06:59:14] Found bcftools - /usr/local/bin/bcftools [06:59:14] Found samtools - /usr/local/bin/samtools [06:59:14] Found java - /usr/local/bin/java [06:59:14] Found snpEff - /usr/local/bin/snpEff [06:59:14] Found samclip - /usr/local/bin/samclip [06:59:14] Found seqtk - /usr/local/bin/seqtk [06:59:14] Found parallel - /usr/local/bin/parallel [06:59:14] Found freebayes - /usr/local/bin/freebayes [06:59:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:59:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:59:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:59:14] Found vcfuniq - /usr/local/bin/vcfuniq [06:59:14] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:59:14] Found gzip - /bin/gzip [06:59:14] Found vt - /usr/local/bin/vt [06:59:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:59:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:59:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:59:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:59:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:59:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:59:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:59:15] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:59:49] This is snippy 4.6.0
Show full stderr[06:59:49] This is snippy 4.6.0 [06:59:49] Written by Torsten Seemann [06:59:49] Obtained from https://github.com/tseemann/snippy [06:59:49] Detected operating system: linux [06:59:49] Enabling bundled linux tools. [06:59:49] Found bwa - /usr/local/bin/bwa [06:59:49] Found bcftools - /usr/local/bin/bcftools [06:59:49] Found samtools - /usr/local/bin/samtools [06:59:49] Found java - /usr/local/bin/java [06:59:49] Found snpEff - /usr/local/bin/snpEff [06:59:49] Found samclip - /usr/local/bin/samclip [06:59:49] Found seqtk - /usr/local/bin/seqtk [06:59:49] Found parallel - /usr/local/bin/parallel [06:59:49] Found freebayes - /usr/local/bin/freebayes [06:59:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:59:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:59:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:59:49] Found vcfuniq - /usr/local/bin/vcfuniq [06:59:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:59:49] Found gzip - /bin/gzip [06:59:49] Found vt - /usr/local/bin/vt [06:59:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:59:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:59:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:59:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:59:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:59:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:59:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:59:49] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:00:34] This is snippy 4.6.0
Show full stderr[07:00:34] This is snippy 4.6.0 [07:00:34] Written by Torsten Seemann [07:00:34] Obtained from https://github.com/tseemann/snippy [07:00:34] Detected operating system: linux [07:00:34] Enabling bundled linux tools. [07:00:34] Found bwa - /usr/local/bin/bwa [07:00:34] Found bcftools - /usr/local/bin/bcftools [07:00:34] Found samtools - /usr/local/bin/samtools [07:00:34] Found java - /usr/local/bin/java [07:00:34] Found snpEff - /usr/local/bin/snpEff [07:00:34] Found samclip - /usr/local/bin/samclip [07:00:34] Found seqtk - /usr/local/bin/seqtk [07:00:34] Found parallel - /usr/local/bin/parallel [07:00:34] Found freebayes - /usr/local/bin/freebayes [07:00:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:00:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:00:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:00:34] Found vcfuniq - /usr/local/bin/vcfuniq [07:00:34] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:00:34] Found gzip - /bin/gzip [07:00:34] Found vt - /usr/local/bin/vt [07:00:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:00:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:00:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:00:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:00:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:00:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:00:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:00:34] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:57:47] This is snippy 4.6.0
Show full stderr[06:57:47] This is snippy 4.6.0 [06:57:47] Written by Torsten Seemann [06:57:47] Obtained from https://github.com/tseemann/snippy [06:57:47] Detected operating system: linux [06:57:47] Enabling bundled linux tools. [06:57:47] Found bwa - /usr/local/bin/bwa [06:57:47] Found bcftools - /usr/local/bin/bcftools [06:57:47] Found samtools - /usr/local/bin/samtools [06:57:47] Found java - /usr/local/bin/java [06:57:47] Found snpEff - /usr/local/bin/snpEff [06:57:47] Found samclip - /usr/local/bin/samclip [06:57:47] Found seqtk - /usr/local/bin/seqtk [06:57:47] Found parallel - /usr/local/bin/parallel [06:57:47] Found freebayes - /usr/local/bin/freebayes [06:57:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:57:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:57:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:57:47] Found vcfuniq - /usr/local/bin/vcfuniq [06:57:47] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:57:47] Found gzip - /bin/gzip [06:57:47] Found vt - /usr/local/bin/vt [06:57:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:57:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:57:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:57:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:57:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:57:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:57:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:57:48] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:58:18] This is snippy 4.6.0
Show full stderr[06:58:18] This is snippy 4.6.0 [06:58:18] Written by Torsten Seemann [06:58:18] Obtained from https://github.com/tseemann/snippy [06:58:18] Detected operating system: linux [06:58:18] Enabling bundled linux tools. [06:58:18] Found bwa - /usr/local/bin/bwa [06:58:18] Found bcftools - /usr/local/bin/bcftools [06:58:18] Found samtools - /usr/local/bin/samtools [06:58:18] Found java - /usr/local/bin/java [06:58:18] Found snpEff - /usr/local/bin/snpEff [06:58:18] Found samclip - /usr/local/bin/samclip [06:58:18] Found seqtk - /usr/local/bin/seqtk [06:58:18] Found parallel - /usr/local/bin/parallel [06:58:18] Found freebayes - /usr/local/bin/freebayes [06:58:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:58:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:58:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:58:18] Found vcfuniq - /usr/local/bin/vcfuniq [06:58:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:58:18] Found gzip - /bin/gzip [06:58:19] Found vt - /usr/local/bin/vt [06:58:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:58:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:58:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:58:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:58:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:58:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:58:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:58:19] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:58:31] This is snippy 4.6.0
Show full stderr[06:58:31] This is snippy 4.6.0 [06:58:31] Written by Torsten Seemann [06:58:31] Obtained from https://github.com/tseemann/snippy [06:58:31] Detected operating system: linux [06:58:31] Enabling bundled linux tools. [06:58:31] Found bwa - /usr/local/bin/bwa [06:58:31] Found bcftools - /usr/local/bin/bcftools [06:58:31] Found samtools - /usr/local/bin/samtools [06:58:31] Found java - /usr/local/bin/java [06:58:31] Found snpEff - /usr/local/bin/snpEff [06:58:31] Found samclip - /usr/local/bin/samclip [06:58:31] Found seqtk - /usr/local/bin/seqtk [06:58:31] Found parallel - /usr/local/bin/parallel [06:58:31] Found freebayes - /usr/local/bin/freebayes [06:58:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:58:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:58:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:58:31] Found vcfuniq - /usr/local/bin/vcfuniq [06:58:31] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:58:31] Found gzip - /bin/gzip [06:58:31] Found vt - /usr/local/bin/vt [06:58:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:58:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:58:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:58:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:58:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:58:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:58:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:58:32] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:58:42] This is snippy 4.6.0
Show full stderr[06:58:42] This is snippy 4.6.0 [06:58:42] Written by Torsten Seemann [06:58:42] Obtained from https://github.com/tseemann/snippy [06:58:42] Detected operating system: linux [06:58:42] Enabling bundled linux tools. [06:58:42] Found bwa - /usr/local/bin/bwa [06:58:43] Found bcftools - /usr/local/bin/bcftools [06:58:43] Found samtools - /usr/local/bin/samtools [06:58:43] Found java - /usr/local/bin/java [06:58:43] Found snpEff - /usr/local/bin/snpEff [06:58:43] Found samclip - /usr/local/bin/samclip [06:58:43] Found seqtk - /usr/local/bin/seqtk [06:58:43] Found parallel - /usr/local/bin/parallel [06:58:43] Found freebayes - /usr/local/bin/freebayes [06:58:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:58:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:58:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:58:43] Found vcfuniq - /usr/local/bin/vcfuniq [06:58:43] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:58:43] Found gzip - /bin/gzip [06:58:43] Found vt - /usr/local/bin/vt [06:58:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:58:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:58:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:58:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:58:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:58:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:58:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:58:43] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:59:01] This is snippy 4.6.0
Show full stderr[06:59:01] This is snippy 4.6.0 [06:59:01] Written by Torsten Seemann [06:59:01] Obtained from https://github.com/tseemann/snippy [06:59:01] Detected operating system: linux [06:59:01] Enabling bundled linux tools. [06:59:01] Found bwa - /usr/local/bin/bwa [06:59:01] Found bcftools - /usr/local/bin/bcftools [06:59:01] Found samtools - /usr/local/bin/samtools [06:59:01] Found java - /usr/local/bin/java [06:59:01] Found snpEff - /usr/local/bin/snpEff [06:59:01] Found samclip - /usr/local/bin/samclip [06:59:01] Found seqtk - /usr/local/bin/seqtk [06:59:01] Found parallel - /usr/local/bin/parallel [06:59:01] Found freebayes - /usr/local/bin/freebayes [06:59:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:59:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:59:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:59:01] Found vcfuniq - /usr/local/bin/vcfuniq [06:59:01] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:59:01] Found gzip - /bin/gzip [06:59:01] Found vt - /usr/local/bin/vt [06:59:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:59:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:59:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:59:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:59:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:59:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:59:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:59:01] Please supply a reference FASTA/GBK/EMBL file with --reference
1[08:03:39] This is snippy 4.6.0
Show full stderr[08:03:39] This is snippy 4.6.0 [08:03:39] Written by Torsten Seemann [08:03:39] Obtained from https://github.com/tseemann/snippy [08:03:39] Detected operating system: linux [08:03:39] Enabling bundled linux tools. [08:03:39] Found bwa - /usr/local/bin/bwa [08:03:39] Found bcftools - /usr/local/bin/bcftools [08:03:39] Found samtools - /usr/local/bin/samtools [08:03:39] Found java - /usr/local/bin/java [08:03:39] Found snpEff - /usr/local/bin/snpEff [08:03:39] Found samclip - /usr/local/bin/samclip [08:03:39] Found seqtk - /usr/local/bin/seqtk [08:03:39] Found parallel - /usr/local/bin/parallel [08:03:39] Found freebayes - /usr/local/bin/freebayes [08:03:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:03:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:03:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:03:39] Found vcfuniq - /usr/local/bin/vcfuniq [08:03:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:03:39] Found gzip - /bin/gzip [08:03:39] Found vt - /usr/local/bin/vt [08:03:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:03:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:03:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:03:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:03:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:03:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:03:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:03:39] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:02:45] This is snippy 4.6.0
Show full stderr[07:02:45] This is snippy 4.6.0 [07:02:45] Written by Torsten Seemann [07:02:45] Obtained from https://github.com/tseemann/snippy [07:02:45] Detected operating system: linux [07:02:45] Enabling bundled linux tools. [07:02:45] Found bwa - /usr/local/bin/bwa [07:02:45] Found bcftools - /usr/local/bin/bcftools [07:02:45] Found samtools - /usr/local/bin/samtools [07:02:45] Found java - /usr/local/bin/java [07:02:45] Found snpEff - /usr/local/bin/snpEff [07:02:45] Found samclip - /usr/local/bin/samclip [07:02:45] Found seqtk - /usr/local/bin/seqtk [07:02:45] Found parallel - /usr/local/bin/parallel [07:02:45] Found freebayes - /usr/local/bin/freebayes [07:02:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:02:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:02:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:02:45] Found vcfuniq - /usr/local/bin/vcfuniq [07:02:45] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:02:45] Found gzip - /bin/gzip [07:02:45] Found vt - /usr/local/bin/vt [07:02:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:02:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:02:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:02:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:02:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:02:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:02:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:02:46] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:03:22] This is snippy 4.6.0
Show full stderr[07:03:22] This is snippy 4.6.0 [07:03:22] Written by Torsten Seemann [07:03:22] Obtained from https://github.com/tseemann/snippy [07:03:22] Detected operating system: linux [07:03:22] Enabling bundled linux tools. [07:03:22] Found bwa - /usr/local/bin/bwa [07:03:22] Found bcftools - /usr/local/bin/bcftools [07:03:22] Found samtools - /usr/local/bin/samtools [07:03:22] Found java - /usr/local/bin/java [07:03:22] Found snpEff - /usr/local/bin/snpEff [07:03:22] Found samclip - /usr/local/bin/samclip [07:03:22] Found seqtk - /usr/local/bin/seqtk [07:03:22] Found parallel - /usr/local/bin/parallel [07:03:22] Found freebayes - /usr/local/bin/freebayes [07:03:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:03:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:03:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:03:22] Found vcfuniq - /usr/local/bin/vcfuniq [07:03:22] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:03:22] Found gzip - /bin/gzip [07:03:22] Found vt - /usr/local/bin/vt [07:03:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:03:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:03:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:03:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:03:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:03:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:03:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:03:23] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:03:25] This is snippy 4.6.0
Show full stderr[07:03:25] This is snippy 4.6.0 [07:03:25] Written by Torsten Seemann [07:03:25] Obtained from https://github.com/tseemann/snippy [07:03:25] Detected operating system: linux [07:03:25] Enabling bundled linux tools. [07:03:25] Found bwa - /usr/local/bin/bwa [07:03:25] Found bcftools - /usr/local/bin/bcftools [07:03:25] Found samtools - /usr/local/bin/samtools [07:03:25] Found java - /usr/local/bin/java [07:03:25] Found snpEff - /usr/local/bin/snpEff [07:03:25] Found samclip - /usr/local/bin/samclip [07:03:25] Found seqtk - /usr/local/bin/seqtk [07:03:25] Found parallel - /usr/local/bin/parallel [07:03:25] Found freebayes - /usr/local/bin/freebayes [07:03:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:03:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:03:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:03:25] Found vcfuniq - /usr/local/bin/vcfuniq [07:03:25] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:03:25] Found gzip - /bin/gzip [07:03:25] Found vt - /usr/local/bin/vt [07:03:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:03:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:03:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:03:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:03:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:03:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:03:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:03:26] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:03:37] This is snippy 4.6.0
Show full stderr[07:03:37] This is snippy 4.6.0 [07:03:37] Written by Torsten Seemann [07:03:37] Obtained from https://github.com/tseemann/snippy [07:03:37] Detected operating system: linux [07:03:37] Enabling bundled linux tools. [07:03:37] Found bwa - /usr/local/bin/bwa [07:03:37] Found bcftools - /usr/local/bin/bcftools [07:03:37] Found samtools - /usr/local/bin/samtools [07:03:37] Found java - /usr/local/bin/java [07:03:37] Found snpEff - /usr/local/bin/snpEff [07:03:37] Found samclip - /usr/local/bin/samclip [07:03:37] Found seqtk - /usr/local/bin/seqtk [07:03:37] Found parallel - /usr/local/bin/parallel [07:03:37] Found freebayes - /usr/local/bin/freebayes [07:03:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:03:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:03:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:03:37] Found vcfuniq - /usr/local/bin/vcfuniq [07:03:37] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:03:37] Found gzip - /bin/gzip [07:03:37] Found vt - /usr/local/bin/vt [07:03:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:03:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:03:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:03:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:03:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:03:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:03:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:03:38] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:04:07] This is snippy 4.6.0
Show full stderr[07:04:07] This is snippy 4.6.0 [07:04:07] Written by Torsten Seemann [07:04:07] Obtained from https://github.com/tseemann/snippy [07:04:07] Detected operating system: linux [07:04:07] Enabling bundled linux tools. [07:04:07] Found bwa - /usr/local/bin/bwa [07:04:07] Found bcftools - /usr/local/bin/bcftools [07:04:07] Found samtools - /usr/local/bin/samtools [07:04:07] Found java - /usr/local/bin/java [07:04:07] Found snpEff - /usr/local/bin/snpEff [07:04:07] Found samclip - /usr/local/bin/samclip [07:04:07] Found seqtk - /usr/local/bin/seqtk [07:04:07] Found parallel - /usr/local/bin/parallel [07:04:07] Found freebayes - /usr/local/bin/freebayes [07:04:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:04:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:04:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:04:07] Found vcfuniq - /usr/local/bin/vcfuniq [07:04:07] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:04:07] Found gzip - /bin/gzip [07:04:07] Found vt - /usr/local/bin/vt [07:04:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:04:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:04:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:04:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:04:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:04:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:04:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:04:08] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:04:28] This is snippy 4.6.0
Show full stderr[07:04:28] This is snippy 4.6.0 [07:04:28] Written by Torsten Seemann [07:04:28] Obtained from https://github.com/tseemann/snippy [07:04:28] Detected operating system: linux [07:04:28] Enabling bundled linux tools. [07:04:28] Found bwa - /usr/local/bin/bwa [07:04:28] Found bcftools - /usr/local/bin/bcftools [07:04:28] Found samtools - /usr/local/bin/samtools [07:04:28] Found java - /usr/local/bin/java [07:04:28] Found snpEff - /usr/local/bin/snpEff [07:04:28] Found samclip - /usr/local/bin/samclip [07:04:28] Found seqtk - /usr/local/bin/seqtk [07:04:28] Found parallel - /usr/local/bin/parallel [07:04:28] Found freebayes - /usr/local/bin/freebayes [07:04:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:04:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:04:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:04:28] Found vcfuniq - /usr/local/bin/vcfuniq [07:04:28] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:04:28] Found gzip - /bin/gzip [07:04:28] Found vt - /usr/local/bin/vt [07:04:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:04:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:04:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:04:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:04:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:04:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:04:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:04:29] Please supply a reference FASTA/GBK/EMBL file with --reference
1[08:03:07] This is snippy 4.6.0
Show full stderr[08:03:07] This is snippy 4.6.0 [08:03:07] Written by Torsten Seemann [08:03:07] Obtained from https://github.com/tseemann/snippy [08:03:07] Detected operating system: linux [08:03:07] Enabling bundled linux tools. [08:03:07] Found bwa - /usr/local/bin/bwa [08:03:07] Found bcftools - /usr/local/bin/bcftools [08:03:07] Found samtools - /usr/local/bin/samtools [08:03:07] Found java - /usr/local/bin/java [08:03:07] Found snpEff - /usr/local/bin/snpEff [08:03:07] Found samclip - /usr/local/bin/samclip [08:03:07] Found seqtk - /usr/local/bin/seqtk [08:03:07] Found parallel - /usr/local/bin/parallel [08:03:07] Found freebayes - /usr/local/bin/freebayes [08:03:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:03:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:03:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:03:07] Found vcfuniq - /usr/local/bin/vcfuniq [08:03:07] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:03:07] Found gzip - /bin/gzip [08:03:07] Found vt - /usr/local/bin/vt [08:03:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:03:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:03:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:03:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:03:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:03:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:03:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:03:08] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:01:39] This is snippy 4.6.0
Show full stderr[07:01:39] This is snippy 4.6.0 [07:01:39] Written by Torsten Seemann [07:01:39] Obtained from https://github.com/tseemann/snippy [07:01:39] Detected operating system: linux [07:01:39] Enabling bundled linux tools. [07:01:39] Found bwa - /usr/local/bin/bwa [07:01:39] Found bcftools - /usr/local/bin/bcftools [07:01:39] Found samtools - /usr/local/bin/samtools [07:01:39] Found java - /usr/local/bin/java [07:01:39] Found snpEff - /usr/local/bin/snpEff [07:01:39] Found samclip - /usr/local/bin/samclip [07:01:39] Found seqtk - /usr/local/bin/seqtk [07:01:39] Found parallel - /usr/local/bin/parallel [07:01:39] Found freebayes - /usr/local/bin/freebayes [07:01:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:01:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:01:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:01:39] Found vcfuniq - /usr/local/bin/vcfuniq [07:01:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:01:39] Found gzip - /bin/gzip [07:01:39] Found vt - /usr/local/bin/vt [07:01:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:01:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:01:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:01:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:01:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:01:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:01:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:01:40] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:03:13] This is snippy 4.6.0
Show full stderr[07:03:13] This is snippy 4.6.0 [07:03:13] Written by Torsten Seemann [07:03:13] Obtained from https://github.com/tseemann/snippy [07:03:13] Detected operating system: linux [07:03:13] Enabling bundled linux tools. [07:03:13] Found bwa - /usr/local/bin/bwa [07:03:13] Found bcftools - /usr/local/bin/bcftools [07:03:13] Found samtools - /usr/local/bin/samtools [07:03:13] Found java - /usr/local/bin/java [07:03:13] Found snpEff - /usr/local/bin/snpEff [07:03:13] Found samclip - /usr/local/bin/samclip [07:03:13] Found seqtk - /usr/local/bin/seqtk [07:03:13] Found parallel - /usr/local/bin/parallel [07:03:13] Found freebayes - /usr/local/bin/freebayes [07:03:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:03:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:03:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:03:13] Found vcfuniq - /usr/local/bin/vcfuniq [07:03:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:03:13] Found gzip - /bin/gzip [07:03:13] Found vt - /usr/local/bin/vt [07:03:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:03:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:03:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:03:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:03:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:03:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:03:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:03:14] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:03:16] This is snippy 4.6.0
Show full stderr[07:03:16] This is snippy 4.6.0 [07:03:16] Written by Torsten Seemann [07:03:16] Obtained from https://github.com/tseemann/snippy [07:03:16] Detected operating system: linux [07:03:16] Enabling bundled linux tools. [07:03:16] Found bwa - /usr/local/bin/bwa [07:03:16] Found bcftools - /usr/local/bin/bcftools [07:03:16] Found samtools - /usr/local/bin/samtools [07:03:16] Found java - /usr/local/bin/java [07:03:16] Found snpEff - /usr/local/bin/snpEff [07:03:16] Found samclip - /usr/local/bin/samclip [07:03:16] Found seqtk - /usr/local/bin/seqtk [07:03:16] Found parallel - /usr/local/bin/parallel [07:03:16] Found freebayes - /usr/local/bin/freebayes [07:03:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:03:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:03:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:03:16] Found vcfuniq - /usr/local/bin/vcfuniq [07:03:16] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:03:16] Found gzip - /bin/gzip [07:03:16] Found vt - /usr/local/bin/vt [07:03:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:03:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:03:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:03:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:03:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:03:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:03:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:03:17] Please supply a reference FASTA/GBK/EMBL file with --reference
1[08:33:36] This is snippy 4.6.0
Show full stderr[08:33:36] This is snippy 4.6.0 [08:33:36] Written by Torsten Seemann [08:33:36] Obtained from https://github.com/tseemann/snippy [08:33:36] Detected operating system: linux [08:33:36] Enabling bundled linux tools. [08:33:36] Found bwa - /usr/local/bin/bwa [08:33:36] Found bcftools - /usr/local/bin/bcftools [08:33:36] Found samtools - /usr/local/bin/samtools [08:33:36] Found java - /usr/local/bin/java [08:33:36] Found snpEff - /usr/local/bin/snpEff [08:33:36] Found samclip - /usr/local/bin/samclip [08:33:36] Found seqtk - /usr/local/bin/seqtk [08:33:36] Found parallel - /usr/local/bin/parallel [08:33:36] Found freebayes - /usr/local/bin/freebayes [08:33:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:33:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:33:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:33:36] Found vcfuniq - /usr/local/bin/vcfuniq [08:33:36] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:33:36] Found gzip - /bin/gzip [08:33:36] Found vt - /usr/local/bin/vt [08:33:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:33:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:33:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:33:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:33:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:33:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:33:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:33:36] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:02:07] This is snippy 4.6.0
Show full stderr[07:02:07] This is snippy 4.6.0 [07:02:07] Written by Torsten Seemann [07:02:07] Obtained from https://github.com/tseemann/snippy [07:02:07] Detected operating system: linux [07:02:07] Enabling bundled linux tools. [07:02:07] Found bwa - /usr/local/bin/bwa [07:02:07] Found bcftools - /usr/local/bin/bcftools [07:02:07] Found samtools - /usr/local/bin/samtools [07:02:07] Found java - /usr/local/bin/java [07:02:07] Found snpEff - /usr/local/bin/snpEff [07:02:07] Found samclip - /usr/local/bin/samclip [07:02:07] Found seqtk - /usr/local/bin/seqtk [07:02:07] Found parallel - /usr/local/bin/parallel [07:02:07] Found freebayes - /usr/local/bin/freebayes [07:02:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:02:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:02:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:02:07] Found vcfuniq - /usr/local/bin/vcfuniq [07:02:07] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:02:07] Found gzip - /bin/gzip [07:02:07] Found vt - /usr/local/bin/vt [07:02:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:02:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:02:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:02:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:02:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:02:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:02:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:02:08] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:02:16] This is snippy 4.6.0
Show full stderr[07:02:16] This is snippy 4.6.0 [07:02:16] Written by Torsten Seemann [07:02:16] Obtained from https://github.com/tseemann/snippy [07:02:16] Detected operating system: linux [07:02:16] Enabling bundled linux tools. [07:02:16] Found bwa - /usr/local/bin/bwa [07:02:16] Found bcftools - /usr/local/bin/bcftools [07:02:16] Found samtools - /usr/local/bin/samtools [07:02:16] Found java - /usr/local/bin/java [07:02:16] Found snpEff - /usr/local/bin/snpEff [07:02:16] Found samclip - /usr/local/bin/samclip [07:02:16] Found seqtk - /usr/local/bin/seqtk [07:02:16] Found parallel - /usr/local/bin/parallel [07:02:16] Found freebayes - /usr/local/bin/freebayes [07:02:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:02:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:02:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:02:16] Found vcfuniq - /usr/local/bin/vcfuniq [07:02:16] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:02:16] Found gzip - /bin/gzip [07:02:16] Found vt - /usr/local/bin/vt [07:02:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:02:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:02:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:02:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:02:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:02:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:02:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:02:17] Please supply a reference FASTA/GBK/EMBL file with --reference
1[08:34:34] This is snippy 4.6.0
Show full stderr[08:34:34] This is snippy 4.6.0 [08:34:34] Written by Torsten Seemann [08:34:34] Obtained from https://github.com/tseemann/snippy [08:34:34] Detected operating system: linux [08:34:34] Enabling bundled linux tools. [08:34:34] Found bwa - /usr/local/bin/bwa [08:34:34] Found bcftools - /usr/local/bin/bcftools [08:34:34] Found samtools - /usr/local/bin/samtools [08:34:34] Found java - /usr/local/bin/java [08:34:34] Found snpEff - /usr/local/bin/snpEff [08:34:34] Found samclip - /usr/local/bin/samclip [08:34:34] Found seqtk - /usr/local/bin/seqtk [08:34:34] Found parallel - /usr/local/bin/parallel [08:34:34] Found freebayes - /usr/local/bin/freebayes [08:34:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:34:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:34:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:34:34] Found vcfuniq - /usr/local/bin/vcfuniq [08:34:34] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:34:34] Found gzip - /bin/gzip [08:34:34] Found vt - /usr/local/bin/vt [08:34:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:34:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:34:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:34:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:34:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:34:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:34:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:34:35] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:38:13] This is snippy 4.6.0
Show full stderr[07:38:13] This is snippy 4.6.0 [07:38:13] Written by Torsten Seemann [07:38:13] Obtained from https://github.com/tseemann/snippy [07:38:13] Detected operating system: linux [07:38:13] Enabling bundled linux tools. [07:38:13] Found bwa - /usr/local/bin/bwa [07:38:13] Found bcftools - /usr/local/bin/bcftools [07:38:13] Found samtools - /usr/local/bin/samtools [07:38:13] Found java - /usr/local/bin/java [07:38:13] Found snpEff - /usr/local/bin/snpEff [07:38:13] Found samclip - /usr/local/bin/samclip [07:38:13] Found seqtk - /usr/local/bin/seqtk [07:38:13] Found parallel - /usr/local/bin/parallel [07:38:13] Found freebayes - /usr/local/bin/freebayes [07:38:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:38:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:38:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:38:13] Found vcfuniq - /usr/local/bin/vcfuniq [07:38:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:38:13] Found gzip - /bin/gzip [07:38:13] Found vt - /usr/local/bin/vt [07:38:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:38:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:38:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:38:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:38:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:38:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:38:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:38:14] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:00:28] This is snippy 4.6.0
Show full stderr[07:00:28] This is snippy 4.6.0 [07:00:28] Written by Torsten Seemann [07:00:28] Obtained from https://github.com/tseemann/snippy [07:00:28] Detected operating system: linux [07:00:28] Enabling bundled linux tools. [07:00:28] Found bwa - /usr/local/bin/bwa [07:00:28] Found bcftools - /usr/local/bin/bcftools [07:00:28] Found samtools - /usr/local/bin/samtools [07:00:28] Found java - /usr/local/bin/java [07:00:28] Found snpEff - /usr/local/bin/snpEff [07:00:28] Found samclip - /usr/local/bin/samclip [07:00:28] Found seqtk - /usr/local/bin/seqtk [07:00:28] Found parallel - /usr/local/bin/parallel [07:00:28] Found freebayes - /usr/local/bin/freebayes [07:00:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:00:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:00:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:00:28] Found vcfuniq - /usr/local/bin/vcfuniq [07:00:28] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:00:28] Found gzip - /bin/gzip [07:00:28] Found vt - /usr/local/bin/vt [07:00:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:00:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:00:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:00:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:00:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:00:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:00:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:00:28] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:00:43] This is snippy 4.6.0
Show full stderr[07:00:43] This is snippy 4.6.0 [07:00:43] Written by Torsten Seemann [07:00:43] Obtained from https://github.com/tseemann/snippy [07:00:43] Detected operating system: linux [07:00:43] Enabling bundled linux tools. [07:00:43] Found bwa - /usr/local/bin/bwa [07:00:43] Found bcftools - /usr/local/bin/bcftools [07:00:43] Found samtools - /usr/local/bin/samtools [07:00:43] Found java - /usr/local/bin/java [07:00:43] Found snpEff - /usr/local/bin/snpEff [07:00:43] Found samclip - /usr/local/bin/samclip [07:00:43] Found seqtk - /usr/local/bin/seqtk [07:00:43] Found parallel - /usr/local/bin/parallel [07:00:43] Found freebayes - /usr/local/bin/freebayes [07:00:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:00:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:00:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:00:43] Found vcfuniq - /usr/local/bin/vcfuniq [07:00:43] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:00:43] Found gzip - /bin/gzip [07:00:43] Found vt - /usr/local/bin/vt [07:00:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:00:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:00:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:00:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:00:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:00:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:00:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:00:43] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:38:56] This is snippy 4.6.0
Show full stderr[07:38:56] This is snippy 4.6.0 [07:38:56] Written by Torsten Seemann [07:38:56] Obtained from https://github.com/tseemann/snippy [07:38:56] Detected operating system: linux [07:38:56] Enabling bundled linux tools. [07:38:56] Found bwa - /usr/local/bin/bwa [07:38:56] Found bcftools - /usr/local/bin/bcftools [07:38:56] Found samtools - /usr/local/bin/samtools [07:38:56] Found java - /usr/local/bin/java [07:38:56] Found snpEff - /usr/local/bin/snpEff [07:38:56] Found samclip - /usr/local/bin/samclip [07:38:56] Found seqtk - /usr/local/bin/seqtk [07:38:56] Found parallel - /usr/local/bin/parallel [07:38:56] Found freebayes - /usr/local/bin/freebayes [07:38:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:38:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:38:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:38:56] Found vcfuniq - /usr/local/bin/vcfuniq [07:38:56] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:38:56] Found gzip - /bin/gzip [07:38:56] Found vt - /usr/local/bin/vt [07:38:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:38:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:38:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:38:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:38:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:38:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:38:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:38:57] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:01:53] This is snippy 4.6.0
Show full stderr[07:01:53] This is snippy 4.6.0 [07:01:53] Written by Torsten Seemann [07:01:53] Obtained from https://github.com/tseemann/snippy [07:01:53] Detected operating system: linux [07:01:53] Enabling bundled linux tools. [07:01:53] Found bwa - /usr/local/bin/bwa [07:01:53] Found bcftools - /usr/local/bin/bcftools [07:01:53] Found samtools - /usr/local/bin/samtools [07:01:53] Found java - /usr/local/bin/java [07:01:53] Found snpEff - /usr/local/bin/snpEff [07:01:53] Found samclip - /usr/local/bin/samclip [07:01:53] Found seqtk - /usr/local/bin/seqtk [07:01:53] Found parallel - /usr/local/bin/parallel [07:01:53] Found freebayes - /usr/local/bin/freebayes [07:01:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:01:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:01:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:01:53] Found vcfuniq - /usr/local/bin/vcfuniq [07:01:53] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:01:53] Found gzip - /bin/gzip [07:01:53] Found vt - /usr/local/bin/vt [07:01:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:01:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:01:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:01:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:01:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:01:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:01:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:01:54] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:02:48] This is snippy 4.6.0
Show full stderr[07:02:48] This is snippy 4.6.0 [07:02:48] Written by Torsten Seemann [07:02:48] Obtained from https://github.com/tseemann/snippy [07:02:48] Detected operating system: linux [07:02:48] Enabling bundled linux tools. [07:02:48] Found bwa - /usr/local/bin/bwa [07:02:48] Found bcftools - /usr/local/bin/bcftools [07:02:48] Found samtools - /usr/local/bin/samtools [07:02:48] Found java - /usr/local/bin/java [07:02:48] Found snpEff - /usr/local/bin/snpEff [07:02:48] Found samclip - /usr/local/bin/samclip [07:02:48] Found seqtk - /usr/local/bin/seqtk [07:02:48] Found parallel - /usr/local/bin/parallel [07:02:48] Found freebayes - /usr/local/bin/freebayes [07:02:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:02:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:02:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:02:48] Found vcfuniq - /usr/local/bin/vcfuniq [07:02:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:02:48] Found gzip - /bin/gzip [07:02:48] Found vt - /usr/local/bin/vt [07:02:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:02:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:02:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:02:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:02:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:02:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:02:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:02:49] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:03:00] This is snippy 4.6.0
Show full stderr[07:03:00] This is snippy 4.6.0 [07:03:00] Written by Torsten Seemann [07:03:00] Obtained from https://github.com/tseemann/snippy [07:03:00] Detected operating system: linux [07:03:00] Enabling bundled linux tools. [07:03:00] Found bwa - /usr/local/bin/bwa [07:03:00] Found bcftools - /usr/local/bin/bcftools [07:03:00] Found samtools - /usr/local/bin/samtools [07:03:00] Found java - /usr/local/bin/java [07:03:00] Found snpEff - /usr/local/bin/snpEff [07:03:00] Found samclip - /usr/local/bin/samclip [07:03:00] Found seqtk - /usr/local/bin/seqtk [07:03:00] Found parallel - /usr/local/bin/parallel [07:03:00] Found freebayes - /usr/local/bin/freebayes [07:03:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:03:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:03:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:03:00] Found vcfuniq - /usr/local/bin/vcfuniq [07:03:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:03:00] Found gzip - /bin/gzip [07:03:00] Found vt - /usr/local/bin/vt [07:03:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:03:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:03:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:03:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:03:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:03:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:03:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:03:01] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:04:14] This is snippy 4.6.0
Show full stderr[07:04:14] This is snippy 4.6.0 [07:04:14] Written by Torsten Seemann [07:04:14] Obtained from https://github.com/tseemann/snippy [07:04:14] Detected operating system: linux [07:04:14] Enabling bundled linux tools. [07:04:14] Found bwa - /usr/local/bin/bwa [07:04:14] Found bcftools - /usr/local/bin/bcftools [07:04:14] Found samtools - /usr/local/bin/samtools [07:04:14] Found java - /usr/local/bin/java [07:04:14] Found snpEff - /usr/local/bin/snpEff [07:04:14] Found samclip - /usr/local/bin/samclip [07:04:14] Found seqtk - /usr/local/bin/seqtk [07:04:14] Found parallel - /usr/local/bin/parallel [07:04:14] Found freebayes - /usr/local/bin/freebayes [07:04:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:04:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:04:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:04:14] Found vcfuniq - /usr/local/bin/vcfuniq [07:04:14] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:04:14] Found gzip - /bin/gzip [07:04:14] Found vt - /usr/local/bin/vt [07:04:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:04:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:04:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:04:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:04:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:04:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:04:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:04:15] Please supply a reference FASTA/GBK/EMBL file with --reference
1[08:09:35] This is snippy 4.6.0
Show full stderr[08:09:35] This is snippy 4.6.0 [08:09:35] Written by Torsten Seemann [08:09:35] Obtained from https://github.com/tseemann/snippy [08:09:35] Detected operating system: linux [08:09:35] Enabling bundled linux tools. [08:09:35] Found bwa - /usr/local/bin/bwa [08:09:35] Found bcftools - /usr/local/bin/bcftools [08:09:35] Found samtools - /usr/local/bin/samtools [08:09:35] Found java - /usr/local/bin/java [08:09:35] Found snpEff - /usr/local/bin/snpEff [08:09:35] Found samclip - /usr/local/bin/samclip [08:09:35] Found seqtk - /usr/local/bin/seqtk [08:09:35] Found parallel - /usr/local/bin/parallel [08:09:35] Found freebayes - /usr/local/bin/freebayes [08:09:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:09:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:09:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:09:35] Found vcfuniq - /usr/local/bin/vcfuniq [08:09:35] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:09:35] Found gzip - /bin/gzip [08:09:35] Found vt - /usr/local/bin/vt [08:09:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:09:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:09:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:09:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:09:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:09:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:09:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:09:36] Please supply a reference FASTA/GBK/EMBL file with --reference
1[08:09:38] This is snippy 4.6.0
Show full stderr[08:09:38] This is snippy 4.6.0 [08:09:38] Written by Torsten Seemann [08:09:38] Obtained from https://github.com/tseemann/snippy [08:09:38] Detected operating system: linux [08:09:38] Enabling bundled linux tools. [08:09:38] Found bwa - /usr/local/bin/bwa [08:09:38] Found bcftools - /usr/local/bin/bcftools [08:09:38] Found samtools - /usr/local/bin/samtools [08:09:38] Found java - /usr/local/bin/java [08:09:38] Found snpEff - /usr/local/bin/snpEff [08:09:38] Found samclip - /usr/local/bin/samclip [08:09:38] Found seqtk - /usr/local/bin/seqtk [08:09:38] Found parallel - /usr/local/bin/parallel [08:09:38] Found freebayes - /usr/local/bin/freebayes [08:09:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:09:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:09:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:09:38] Found vcfuniq - /usr/local/bin/vcfuniq [08:09:38] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:09:38] Found gzip - /bin/gzip [08:09:38] Found vt - /usr/local/bin/vt [08:09:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:09:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:09:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:09:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:09:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:09:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:09:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:09:39] Please supply a reference FASTA/GBK/EMBL file with --reference
1[08:09:44] This is snippy 4.6.0
Show full stderr[08:09:44] This is snippy 4.6.0 [08:09:44] Written by Torsten Seemann [08:09:44] Obtained from https://github.com/tseemann/snippy [08:09:44] Detected operating system: linux [08:09:44] Enabling bundled linux tools. [08:09:44] Found bwa - /usr/local/bin/bwa [08:09:44] Found bcftools - /usr/local/bin/bcftools [08:09:44] Found samtools - /usr/local/bin/samtools [08:09:44] Found java - /usr/local/bin/java [08:09:44] Found snpEff - /usr/local/bin/snpEff [08:09:44] Found samclip - /usr/local/bin/samclip [08:09:44] Found seqtk - /usr/local/bin/seqtk [08:09:44] Found parallel - /usr/local/bin/parallel [08:09:44] Found freebayes - /usr/local/bin/freebayes [08:09:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:09:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:09:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:09:44] Found vcfuniq - /usr/local/bin/vcfuniq [08:09:44] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:09:44] Found gzip - /bin/gzip [08:09:44] Found vt - /usr/local/bin/vt [08:09:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:09:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:09:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:09:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:09:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:09:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:09:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:09:52] Please supply a reference FASTA/GBK/EMBL file with --reference
1[08:16:38] This is snippy 4.6.0
Show full stderr[08:16:38] This is snippy 4.6.0 [08:16:38] Written by Torsten Seemann [08:16:38] Obtained from https://github.com/tseemann/snippy [08:16:38] Detected operating system: linux [08:16:38] Enabling bundled linux tools. [08:16:38] Found bwa - /usr/local/bin/bwa [08:16:38] Found bcftools - /usr/local/bin/bcftools [08:16:38] Found samtools - /usr/local/bin/samtools [08:16:38] Found java - /usr/local/bin/java [08:16:38] Found snpEff - /usr/local/bin/snpEff [08:16:38] Found samclip - /usr/local/bin/samclip [08:16:38] Found seqtk - /usr/local/bin/seqtk [08:16:38] Found parallel - /usr/local/bin/parallel [08:16:38] Found freebayes - /usr/local/bin/freebayes [08:16:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:16:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:16:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:16:38] Found vcfuniq - /usr/local/bin/vcfuniq [08:16:38] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:16:38] Found gzip - /bin/gzip [08:16:38] Found vt - /usr/local/bin/vt [08:16:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:16:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:16:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:16:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:16:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:16:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:16:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:16:39] Please supply a reference FASTA/GBK/EMBL file with --reference
1[08:21:31] This is snippy 4.6.0
Show full stderr[08:21:31] This is snippy 4.6.0 [08:21:31] Written by Torsten Seemann [08:21:31] Obtained from https://github.com/tseemann/snippy [08:21:31] Detected operating system: linux [08:21:31] Enabling bundled linux tools. [08:21:32] Found bwa - /usr/local/bin/bwa [08:21:32] Found bcftools - /usr/local/bin/bcftools [08:21:32] Found samtools - /usr/local/bin/samtools [08:21:32] Found java - /usr/local/bin/java [08:21:32] Found snpEff - /usr/local/bin/snpEff [08:21:32] Found samclip - /usr/local/bin/samclip [08:21:32] Found seqtk - /usr/local/bin/seqtk [08:21:32] Found parallel - /usr/local/bin/parallel [08:21:32] Found freebayes - /usr/local/bin/freebayes [08:21:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:21:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:21:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:21:32] Found vcfuniq - /usr/local/bin/vcfuniq [08:21:32] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:21:32] Found gzip - /bin/gzip [08:21:32] Found vt - /usr/local/bin/vt [08:21:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:21:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:21:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:21:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:21:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:21:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:21:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:21:32] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:06:04] This is snippy 4.6.0
Show full stderr[07:06:04] This is snippy 4.6.0 [07:06:04] Written by Torsten Seemann [07:06:04] Obtained from https://github.com/tseemann/snippy [07:06:04] Detected operating system: linux [07:06:04] Enabling bundled linux tools. [07:06:04] Found bwa - /usr/local/bin/bwa [07:06:04] Found bcftools - /usr/local/bin/bcftools [07:06:04] Found samtools - /usr/local/bin/samtools [07:06:04] Found java - /usr/local/bin/java [07:06:04] Found snpEff - /usr/local/bin/snpEff [07:06:04] Found samclip - /usr/local/bin/samclip [07:06:04] Found seqtk - /usr/local/bin/seqtk [07:06:04] Found parallel - /usr/local/bin/parallel [07:06:04] Found freebayes - /usr/local/bin/freebayes [07:06:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:06:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:06:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:06:04] Found vcfuniq - /usr/local/bin/vcfuniq [07:06:04] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:06:04] Found gzip - /bin/gzip [07:06:04] Found vt - /usr/local/bin/vt [07:06:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:06:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:06:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:06:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:06:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:06:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:06:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:06:05] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:03:28] This is snippy 4.6.0
Show full stderr[07:03:28] This is snippy 4.6.0 [07:03:28] Written by Torsten Seemann [07:03:28] Obtained from https://github.com/tseemann/snippy [07:03:28] Detected operating system: linux [07:03:28] Enabling bundled linux tools. [07:03:28] Found bwa - /usr/local/bin/bwa [07:03:28] Found bcftools - /usr/local/bin/bcftools [07:03:28] Found samtools - /usr/local/bin/samtools [07:03:28] Found java - /usr/local/bin/java [07:03:28] Found snpEff - /usr/local/bin/snpEff [07:03:28] Found samclip - /usr/local/bin/samclip [07:03:28] Found seqtk - /usr/local/bin/seqtk [07:03:28] Found parallel - /usr/local/bin/parallel [07:03:28] Found freebayes - /usr/local/bin/freebayes [07:03:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:03:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:03:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:03:28] Found vcfuniq - /usr/local/bin/vcfuniq [07:03:28] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:03:28] Found gzip - /bin/gzip [07:03:28] Found vt - /usr/local/bin/vt [07:03:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:03:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:03:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:03:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:03:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:03:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:03:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:03:29] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:03:34] This is snippy 4.6.0
Show full stderr[07:03:34] This is snippy 4.6.0 [07:03:34] Written by Torsten Seemann [07:03:34] Obtained from https://github.com/tseemann/snippy [07:03:34] Detected operating system: linux [07:03:34] Enabling bundled linux tools. [07:03:34] Found bwa - /usr/local/bin/bwa [07:03:34] Found bcftools - /usr/local/bin/bcftools [07:03:34] Found samtools - /usr/local/bin/samtools [07:03:34] Found java - /usr/local/bin/java [07:03:34] Found snpEff - /usr/local/bin/snpEff [07:03:34] Found samclip - /usr/local/bin/samclip [07:03:34] Found seqtk - /usr/local/bin/seqtk [07:03:34] Found parallel - /usr/local/bin/parallel [07:03:34] Found freebayes - /usr/local/bin/freebayes [07:03:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:03:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:03:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:03:34] Found vcfuniq - /usr/local/bin/vcfuniq [07:03:34] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:03:34] Found gzip - /bin/gzip [07:03:34] Found vt - /usr/local/bin/vt [07:03:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:03:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:03:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:03:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:03:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:03:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:03:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:03:35] Please supply a reference FASTA/GBK/EMBL file with --reference
1[08:09:25] This is snippy 4.6.0
Show full stderr[08:09:25] This is snippy 4.6.0 [08:09:25] Written by Torsten Seemann [08:09:25] Obtained from https://github.com/tseemann/snippy [08:09:25] Detected operating system: linux [08:09:25] Enabling bundled linux tools. [08:09:25] Found bwa - /usr/local/bin/bwa [08:09:25] Found bcftools - /usr/local/bin/bcftools [08:09:25] Found samtools - /usr/local/bin/samtools [08:09:25] Found java - /usr/local/bin/java [08:09:25] Found snpEff - /usr/local/bin/snpEff [08:09:25] Found samclip - /usr/local/bin/samclip [08:09:25] Found seqtk - /usr/local/bin/seqtk [08:09:25] Found parallel - /usr/local/bin/parallel [08:09:25] Found freebayes - /usr/local/bin/freebayes [08:09:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:09:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:09:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:09:25] Found vcfuniq - /usr/local/bin/vcfuniq [08:09:25] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:09:25] Found gzip - /bin/gzip [08:09:25] Found vt - /usr/local/bin/vt [08:09:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:09:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:09:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:09:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:09:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:09:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:09:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:09:31] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:03:40] This is snippy 4.6.0
Show full stderr[07:03:40] This is snippy 4.6.0 [07:03:40] Written by Torsten Seemann [07:03:40] Obtained from https://github.com/tseemann/snippy [07:03:40] Detected operating system: linux [07:03:40] Enabling bundled linux tools. [07:03:40] Found bwa - /usr/local/bin/bwa [07:03:40] Found bcftools - /usr/local/bin/bcftools [07:03:40] Found samtools - /usr/local/bin/samtools [07:03:40] Found java - /usr/local/bin/java [07:03:40] Found snpEff - /usr/local/bin/snpEff [07:03:40] Found samclip - /usr/local/bin/samclip [07:03:40] Found seqtk - /usr/local/bin/seqtk [07:03:40] Found parallel - /usr/local/bin/parallel [07:03:40] Found freebayes - /usr/local/bin/freebayes [07:03:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:03:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:03:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:03:40] Found vcfuniq - /usr/local/bin/vcfuniq [07:03:40] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:03:40] Found gzip - /bin/gzip [07:03:40] Found vt - /usr/local/bin/vt [07:03:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:03:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:03:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:03:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:03:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:03:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:03:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:03:41] Please supply a reference FASTA/GBK/EMBL file with --reference
1[08:16:35] This is snippy 4.6.0
Show full stderr[08:16:35] This is snippy 4.6.0 [08:16:35] Written by Torsten Seemann [08:16:35] Obtained from https://github.com/tseemann/snippy [08:16:35] Detected operating system: linux [08:16:35] Enabling bundled linux tools. [08:16:35] Found bwa - /usr/local/bin/bwa [08:16:35] Found bcftools - /usr/local/bin/bcftools [08:16:35] Found samtools - /usr/local/bin/samtools [08:16:35] Found java - /usr/local/bin/java [08:16:35] Found snpEff - /usr/local/bin/snpEff [08:16:35] Found samclip - /usr/local/bin/samclip [08:16:35] Found seqtk - /usr/local/bin/seqtk [08:16:35] Found parallel - /usr/local/bin/parallel [08:16:35] Found freebayes - /usr/local/bin/freebayes [08:16:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:16:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:16:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:16:35] Found vcfuniq - /usr/local/bin/vcfuniq [08:16:35] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:16:35] Found gzip - /bin/gzip [08:16:35] Found vt - /usr/local/bin/vt [08:16:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:16:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:16:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:16:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:16:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:16:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:16:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:16:36] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:03:43] This is snippy 4.6.0
Show full stderr[07:03:43] This is snippy 4.6.0 [07:03:43] Written by Torsten Seemann [07:03:43] Obtained from https://github.com/tseemann/snippy [07:03:43] Detected operating system: linux [07:03:43] Enabling bundled linux tools. [07:03:43] Found bwa - /usr/local/bin/bwa [07:03:43] Found bcftools - /usr/local/bin/bcftools [07:03:43] Found samtools - /usr/local/bin/samtools [07:03:43] Found java - /usr/local/bin/java [07:03:43] Found snpEff - /usr/local/bin/snpEff [07:03:43] Found samclip - /usr/local/bin/samclip [07:03:43] Found seqtk - /usr/local/bin/seqtk [07:03:43] Found parallel - /usr/local/bin/parallel [07:03:43] Found freebayes - /usr/local/bin/freebayes [07:03:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:03:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:03:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:03:43] Found vcfuniq - /usr/local/bin/vcfuniq [07:03:43] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:03:43] Found gzip - /bin/gzip [07:03:43] Found vt - /usr/local/bin/vt [07:03:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:03:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:03:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:03:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:03:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:03:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:03:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:03:44] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:03:52] This is snippy 4.6.0
Show full stderr[07:03:52] This is snippy 4.6.0 [07:03:52] Written by Torsten Seemann [07:03:52] Obtained from https://github.com/tseemann/snippy [07:03:52] Detected operating system: linux [07:03:52] Enabling bundled linux tools. [07:03:52] Found bwa - /usr/local/bin/bwa [07:03:52] Found bcftools - /usr/local/bin/bcftools [07:03:52] Found samtools - /usr/local/bin/samtools [07:03:52] Found java - /usr/local/bin/java [07:03:52] Found snpEff - /usr/local/bin/snpEff [07:03:52] Found samclip - /usr/local/bin/samclip [07:03:52] Found seqtk - /usr/local/bin/seqtk [07:03:52] Found parallel - /usr/local/bin/parallel [07:03:52] Found freebayes - /usr/local/bin/freebayes [07:03:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:03:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:03:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:03:52] Found vcfuniq - /usr/local/bin/vcfuniq [07:03:52] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:03:52] Found gzip - /bin/gzip [07:03:52] Found vt - /usr/local/bin/vt [07:03:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:03:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:03:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:03:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:03:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:03:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:03:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:03:53] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:04:01] This is snippy 4.6.0
Show full stderr[07:04:01] This is snippy 4.6.0 [07:04:01] Written by Torsten Seemann [07:04:01] Obtained from https://github.com/tseemann/snippy [07:04:01] Detected operating system: linux [07:04:01] Enabling bundled linux tools. [07:04:01] Found bwa - /usr/local/bin/bwa [07:04:01] Found bcftools - /usr/local/bin/bcftools [07:04:01] Found samtools - /usr/local/bin/samtools [07:04:01] Found java - /usr/local/bin/java [07:04:01] Found snpEff - /usr/local/bin/snpEff [07:04:01] Found samclip - /usr/local/bin/samclip [07:04:01] Found seqtk - /usr/local/bin/seqtk [07:04:01] Found parallel - /usr/local/bin/parallel [07:04:01] Found freebayes - /usr/local/bin/freebayes [07:04:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:04:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:04:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:04:01] Found vcfuniq - /usr/local/bin/vcfuniq [07:04:01] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:04:01] Found gzip - /bin/gzip [07:04:01] Found vt - /usr/local/bin/vt [07:04:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:04:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:04:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:04:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:04:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:04:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:04:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:04:02] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:04:22] This is snippy 4.6.0
Show full stderr[07:04:22] This is snippy 4.6.0 [07:04:22] Written by Torsten Seemann [07:04:22] Obtained from https://github.com/tseemann/snippy [07:04:22] Detected operating system: linux [07:04:22] Enabling bundled linux tools. [07:04:22] Found bwa - /usr/local/bin/bwa [07:04:22] Found bcftools - /usr/local/bin/bcftools [07:04:22] Found samtools - /usr/local/bin/samtools [07:04:22] Found java - /usr/local/bin/java [07:04:22] Found snpEff - /usr/local/bin/snpEff [07:04:22] Found samclip - /usr/local/bin/samclip [07:04:22] Found seqtk - /usr/local/bin/seqtk [07:04:22] Found parallel - /usr/local/bin/parallel [07:04:22] Found freebayes - /usr/local/bin/freebayes [07:04:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:04:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:04:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:04:22] Found vcfuniq - /usr/local/bin/vcfuniq [07:04:22] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:04:22] Found gzip - /bin/gzip [07:04:22] Found vt - /usr/local/bin/vt [07:04:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:04:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:04:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:04:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:04:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:04:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:04:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:04:23] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:04:37] This is snippy 4.6.0
Show full stderr[07:04:37] This is snippy 4.6.0 [07:04:37] Written by Torsten Seemann [07:04:37] Obtained from https://github.com/tseemann/snippy [07:04:37] Detected operating system: linux [07:04:37] Enabling bundled linux tools. [07:04:37] Found bwa - /usr/local/bin/bwa [07:04:37] Found bcftools - /usr/local/bin/bcftools [07:04:37] Found samtools - /usr/local/bin/samtools [07:04:37] Found java - /usr/local/bin/java [07:04:37] Found snpEff - /usr/local/bin/snpEff [07:04:37] Found samclip - /usr/local/bin/samclip [07:04:37] Found seqtk - /usr/local/bin/seqtk [07:04:37] Found parallel - /usr/local/bin/parallel [07:04:37] Found freebayes - /usr/local/bin/freebayes [07:04:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:04:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:04:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:04:37] Found vcfuniq - /usr/local/bin/vcfuniq [07:04:37] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:04:37] Found gzip - /bin/gzip [07:04:37] Found vt - /usr/local/bin/vt [07:04:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:04:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:04:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:04:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:04:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:04:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:04:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:04:38] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:04:43] This is snippy 4.6.0
Show full stderr[07:04:43] This is snippy 4.6.0 [07:04:43] Written by Torsten Seemann [07:04:43] Obtained from https://github.com/tseemann/snippy [07:04:43] Detected operating system: linux [07:04:43] Enabling bundled linux tools. [07:04:43] Found bwa - /usr/local/bin/bwa [07:04:43] Found bcftools - /usr/local/bin/bcftools [07:04:43] Found samtools - /usr/local/bin/samtools [07:04:43] Found java - /usr/local/bin/java [07:04:43] Found snpEff - /usr/local/bin/snpEff [07:04:43] Found samclip - /usr/local/bin/samclip [07:04:43] Found seqtk - /usr/local/bin/seqtk [07:04:43] Found parallel - /usr/local/bin/parallel [07:04:43] Found freebayes - /usr/local/bin/freebayes [07:04:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:04:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:04:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:04:43] Found vcfuniq - /usr/local/bin/vcfuniq [07:04:43] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:04:43] Found gzip - /bin/gzip [07:04:43] Found vt - /usr/local/bin/vt [07:04:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:04:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:04:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:04:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:04:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:04:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:04:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:04:44] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:04:52] This is snippy 4.6.0
Show full stderr[07:04:52] This is snippy 4.6.0 [07:04:52] Written by Torsten Seemann [07:04:52] Obtained from https://github.com/tseemann/snippy [07:04:52] Detected operating system: linux [07:04:52] Enabling bundled linux tools. [07:04:52] Found bwa - /usr/local/bin/bwa [07:04:52] Found bcftools - /usr/local/bin/bcftools [07:04:52] Found samtools - /usr/local/bin/samtools [07:04:52] Found java - /usr/local/bin/java [07:04:52] Found snpEff - /usr/local/bin/snpEff [07:04:52] Found samclip - /usr/local/bin/samclip [07:04:52] Found seqtk - /usr/local/bin/seqtk [07:04:52] Found parallel - /usr/local/bin/parallel [07:04:52] Found freebayes - /usr/local/bin/freebayes [07:04:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:04:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:04:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:04:52] Found vcfuniq - /usr/local/bin/vcfuniq [07:04:52] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:04:52] Found gzip - /bin/gzip [07:04:52] Found vt - /usr/local/bin/vt [07:04:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:04:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:04:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:04:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:04:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:04:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:04:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:04:53] Please supply a reference FASTA/GBK/EMBL file with --reference
1[08:16:51] This is snippy 4.6.0
Show full stderr[08:16:51] This is snippy 4.6.0 [08:16:51] Written by Torsten Seemann [08:16:51] Obtained from https://github.com/tseemann/snippy [08:16:51] Detected operating system: linux [08:16:51] Enabling bundled linux tools. [08:16:51] Found bwa - /usr/local/bin/bwa [08:16:51] Found bcftools - /usr/local/bin/bcftools [08:16:51] Found samtools - /usr/local/bin/samtools [08:16:51] Found java - /usr/local/bin/java [08:16:51] Found snpEff - /usr/local/bin/snpEff [08:16:51] Found samclip - /usr/local/bin/samclip [08:16:51] Found seqtk - /usr/local/bin/seqtk [08:16:51] Found parallel - /usr/local/bin/parallel [08:16:51] Found freebayes - /usr/local/bin/freebayes [08:16:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:16:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:16:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:16:51] Found vcfuniq - /usr/local/bin/vcfuniq [08:16:51] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:16:51] Found gzip - /bin/gzip [08:16:51] Found vt - /usr/local/bin/vt [08:16:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:16:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:16:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:16:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:16:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:16:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:16:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:16:52] Please supply a reference FASTA/GBK/EMBL file with --reference
1[08:22:52] This is snippy 4.6.0
Show full stderr[08:22:52] This is snippy 4.6.0 [08:22:52] Written by Torsten Seemann [08:22:52] Obtained from https://github.com/tseemann/snippy [08:22:52] Detected operating system: linux [08:22:52] Enabling bundled linux tools. [08:22:52] Found bwa - /usr/local/bin/bwa [08:22:52] Found bcftools - /usr/local/bin/bcftools [08:22:52] Found samtools - /usr/local/bin/samtools [08:22:52] Found java - /usr/local/bin/java [08:22:52] Found snpEff - /usr/local/bin/snpEff [08:22:52] Found samclip - /usr/local/bin/samclip [08:22:52] Found seqtk - /usr/local/bin/seqtk [08:22:52] Found parallel - /usr/local/bin/parallel [08:22:52] Found freebayes - /usr/local/bin/freebayes [08:22:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:22:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:22:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:22:52] Found vcfuniq - /usr/local/bin/vcfuniq [08:22:52] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:22:52] Found gzip - /bin/gzip [08:22:52] Found vt - /usr/local/bin/vt [08:22:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:22:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:22:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:22:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:22:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:22:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:22:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:22:52] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:05:04] This is snippy 4.6.0
Show full stderr[07:05:04] This is snippy 4.6.0 [07:05:04] Written by Torsten Seemann [07:05:04] Obtained from https://github.com/tseemann/snippy [07:05:04] Detected operating system: linux [07:05:04] Enabling bundled linux tools. [07:05:04] Found bwa - /usr/local/bin/bwa [07:05:04] Found bcftools - /usr/local/bin/bcftools [07:05:04] Found samtools - /usr/local/bin/samtools [07:05:04] Found java - /usr/local/bin/java [07:05:04] Found snpEff - /usr/local/bin/snpEff [07:05:04] Found samclip - /usr/local/bin/samclip [07:05:04] Found seqtk - /usr/local/bin/seqtk [07:05:04] Found parallel - /usr/local/bin/parallel [07:05:04] Found freebayes - /usr/local/bin/freebayes [07:05:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:05:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:05:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:05:04] Found vcfuniq - /usr/local/bin/vcfuniq [07:05:04] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:05:04] Found gzip - /bin/gzip [07:05:04] Found vt - /usr/local/bin/vt [07:05:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:05:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:05:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:05:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:05:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:05:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:05:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:05:05] Please supply a reference FASTA/GBK/EMBL file with --reference
1[08:39:33] This is snippy 4.6.0
Show full stderr[08:39:33] This is snippy 4.6.0 [08:39:33] Written by Torsten Seemann [08:39:33] Obtained from https://github.com/tseemann/snippy [08:39:33] Detected operating system: linux [08:39:33] Enabling bundled linux tools. [08:39:33] Found bwa - /usr/local/bin/bwa [08:39:33] Found bcftools - /usr/local/bin/bcftools [08:39:33] Found samtools - /usr/local/bin/samtools [08:39:33] Found java - /usr/local/bin/java [08:39:33] Found snpEff - /usr/local/bin/snpEff [08:39:33] Found samclip - /usr/local/bin/samclip [08:39:33] Found seqtk - /usr/local/bin/seqtk [08:39:33] Found parallel - /usr/local/bin/parallel [08:39:33] Found freebayes - /usr/local/bin/freebayes [08:39:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:39:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:39:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:39:34] Found vcfuniq - /usr/local/bin/vcfuniq [08:39:34] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:39:34] Found gzip - /bin/gzip [08:39:34] Found vt - /usr/local/bin/vt [08:39:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:39:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:39:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:39:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:39:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:39:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:39:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:39:34] Please supply a reference FASTA/GBK/EMBL file with --reference
1[08:40:35] This is snippy 4.6.0
Show full stderr[08:40:35] This is snippy 4.6.0 [08:40:35] Written by Torsten Seemann [08:40:35] Obtained from https://github.com/tseemann/snippy [08:40:35] Detected operating system: linux [08:40:35] Enabling bundled linux tools. [08:40:35] Found bwa - /usr/local/bin/bwa [08:40:35] Found bcftools - /usr/local/bin/bcftools [08:40:35] Found samtools - /usr/local/bin/samtools [08:40:35] Found java - /usr/local/bin/java [08:40:35] Found snpEff - /usr/local/bin/snpEff [08:40:35] Found samclip - /usr/local/bin/samclip [08:40:35] Found seqtk - /usr/local/bin/seqtk [08:40:35] Found parallel - /usr/local/bin/parallel [08:40:35] Found freebayes - /usr/local/bin/freebayes [08:40:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:40:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:40:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:40:35] Found vcfuniq - /usr/local/bin/vcfuniq [08:40:35] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:40:35] Found gzip - /bin/gzip [08:40:35] Found vt - /usr/local/bin/vt [08:40:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:40:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:40:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:40:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:40:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:40:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:40:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:40:35] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:03:03] This is snippy 4.6.0
Show full stderr[07:03:03] This is snippy 4.6.0 [07:03:03] Written by Torsten Seemann [07:03:03] Obtained from https://github.com/tseemann/snippy [07:03:03] Detected operating system: linux [07:03:03] Enabling bundled linux tools. [07:03:03] Found bwa - /usr/local/bin/bwa [07:03:03] Found bcftools - /usr/local/bin/bcftools [07:03:03] Found samtools - /usr/local/bin/samtools [07:03:03] Found java - /usr/local/bin/java [07:03:03] Found snpEff - /usr/local/bin/snpEff [07:03:03] Found samclip - /usr/local/bin/samclip [07:03:03] Found seqtk - /usr/local/bin/seqtk [07:03:03] Found parallel - /usr/local/bin/parallel [07:03:03] Found freebayes - /usr/local/bin/freebayes [07:03:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:03:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:03:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:03:03] Found vcfuniq - /usr/local/bin/vcfuniq [07:03:03] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:03:03] Found gzip - /bin/gzip [07:03:03] Found vt - /usr/local/bin/vt [07:03:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:03:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:03:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:03:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:03:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:03:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:03:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:03:04] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:03:46] This is snippy 4.6.0
Show full stderr[07:03:46] This is snippy 4.6.0 [07:03:46] Written by Torsten Seemann [07:03:46] Obtained from https://github.com/tseemann/snippy [07:03:46] Detected operating system: linux [07:03:46] Enabling bundled linux tools. [07:03:46] Found bwa - /usr/local/bin/bwa [07:03:46] Found bcftools - /usr/local/bin/bcftools [07:03:46] Found samtools - /usr/local/bin/samtools [07:03:46] Found java - /usr/local/bin/java [07:03:46] Found snpEff - /usr/local/bin/snpEff [07:03:46] Found samclip - /usr/local/bin/samclip [07:03:46] Found seqtk - /usr/local/bin/seqtk [07:03:46] Found parallel - /usr/local/bin/parallel [07:03:46] Found freebayes - /usr/local/bin/freebayes [07:03:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:03:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:03:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:03:46] Found vcfuniq - /usr/local/bin/vcfuniq [07:03:46] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:03:46] Found gzip - /bin/gzip [07:03:46] Found vt - /usr/local/bin/vt [07:03:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:03:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:03:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:03:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:03:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:03:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:03:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:03:47] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:06:56] This is snippy 4.6.0
Show full stderr[07:06:56] This is snippy 4.6.0 [07:06:56] Written by Torsten Seemann [07:06:56] Obtained from https://github.com/tseemann/snippy [07:06:56] Detected operating system: linux [07:06:56] Enabling bundled linux tools. [07:06:56] Found bwa - /usr/local/bin/bwa [07:06:56] Found bcftools - /usr/local/bin/bcftools [07:06:56] Found samtools - /usr/local/bin/samtools [07:06:56] Found java - /usr/local/bin/java [07:06:56] Found snpEff - /usr/local/bin/snpEff [07:06:56] Found samclip - /usr/local/bin/samclip [07:06:56] Found seqtk - /usr/local/bin/seqtk [07:06:56] Found parallel - /usr/local/bin/parallel [07:06:56] Found freebayes - /usr/local/bin/freebayes [07:06:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:06:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:06:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:06:56] Found vcfuniq - /usr/local/bin/vcfuniq [07:06:56] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:06:56] Found gzip - /bin/gzip [07:06:56] Found vt - /usr/local/bin/vt [07:06:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:06:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:06:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:06:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:06:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:06:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:06:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:06:57] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:07:02] This is snippy 4.6.0
Show full stderr[07:07:02] This is snippy 4.6.0 [07:07:02] Written by Torsten Seemann [07:07:02] Obtained from https://github.com/tseemann/snippy [07:07:02] Detected operating system: linux [07:07:02] Enabling bundled linux tools. [07:07:02] Found bwa - /usr/local/bin/bwa [07:07:02] Found bcftools - /usr/local/bin/bcftools [07:07:02] Found samtools - /usr/local/bin/samtools [07:07:02] Found java - /usr/local/bin/java [07:07:02] Found snpEff - /usr/local/bin/snpEff [07:07:02] Found samclip - /usr/local/bin/samclip [07:07:02] Found seqtk - /usr/local/bin/seqtk [07:07:02] Found parallel - /usr/local/bin/parallel [07:07:02] Found freebayes - /usr/local/bin/freebayes [07:07:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:07:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:07:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:07:02] Found vcfuniq - /usr/local/bin/vcfuniq [07:07:02] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:07:02] Found gzip - /bin/gzip [07:07:02] Found vt - /usr/local/bin/vt [07:07:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:07:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:07:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:07:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:07:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:07:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:07:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:07:03] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:07:16] This is snippy 4.6.0
Show full stderr[07:07:16] This is snippy 4.6.0 [07:07:16] Written by Torsten Seemann [07:07:16] Obtained from https://github.com/tseemann/snippy [07:07:16] Detected operating system: linux [07:07:16] Enabling bundled linux tools. [07:07:16] Found bwa - /usr/local/bin/bwa [07:07:16] Found bcftools - /usr/local/bin/bcftools [07:07:16] Found samtools - /usr/local/bin/samtools [07:07:16] Found java - /usr/local/bin/java [07:07:16] Found snpEff - /usr/local/bin/snpEff [07:07:16] Found samclip - /usr/local/bin/samclip [07:07:16] Found seqtk - /usr/local/bin/seqtk [07:07:16] Found parallel - /usr/local/bin/parallel [07:07:16] Found freebayes - /usr/local/bin/freebayes [07:07:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:07:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:07:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:07:16] Found vcfuniq - /usr/local/bin/vcfuniq [07:07:16] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:07:16] Found gzip - /bin/gzip [07:07:16] Found vt - /usr/local/bin/vt [07:07:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:07:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:07:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:07:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:07:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:07:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:07:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:07:17] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:07:31] This is snippy 4.6.0
Show full stderr[07:07:31] This is snippy 4.6.0 [07:07:31] Written by Torsten Seemann [07:07:31] Obtained from https://github.com/tseemann/snippy [07:07:31] Detected operating system: linux [07:07:31] Enabling bundled linux tools. [07:07:31] Found bwa - /usr/local/bin/bwa [07:07:31] Found bcftools - /usr/local/bin/bcftools [07:07:31] Found samtools - /usr/local/bin/samtools [07:07:31] Found java - /usr/local/bin/java [07:07:31] Found snpEff - /usr/local/bin/snpEff [07:07:31] Found samclip - /usr/local/bin/samclip [07:07:31] Found seqtk - /usr/local/bin/seqtk [07:07:31] Found parallel - /usr/local/bin/parallel [07:07:31] Found freebayes - /usr/local/bin/freebayes [07:07:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:07:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:07:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:07:31] Found vcfuniq - /usr/local/bin/vcfuniq [07:07:31] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:07:31] Found gzip - /bin/gzip [07:07:31] Found vt - /usr/local/bin/vt [07:07:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:07:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:07:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:07:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:07:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:07:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:07:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:07:32] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:07:56] This is snippy 4.6.0
Show full stderr[07:07:56] This is snippy 4.6.0 [07:07:56] Written by Torsten Seemann [07:07:56] Obtained from https://github.com/tseemann/snippy [07:07:56] Detected operating system: linux [07:07:56] Enabling bundled linux tools. [07:07:56] Found bwa - /usr/local/bin/bwa [07:07:56] Found bcftools - /usr/local/bin/bcftools [07:07:56] Found samtools - /usr/local/bin/samtools [07:07:56] Found java - /usr/local/bin/java [07:07:56] Found snpEff - /usr/local/bin/snpEff [07:07:56] Found samclip - /usr/local/bin/samclip [07:07:56] Found seqtk - /usr/local/bin/seqtk [07:07:56] Found parallel - /usr/local/bin/parallel [07:07:56] Found freebayes - /usr/local/bin/freebayes [07:07:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:07:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:07:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:07:56] Found vcfuniq - /usr/local/bin/vcfuniq [07:07:56] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:07:56] Found gzip - /bin/gzip [07:07:56] Found vt - /usr/local/bin/vt [07:07:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:07:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:07:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:07:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:07:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:07:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:07:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:07:57] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:08:04] This is snippy 4.6.0
Show full stderr[07:08:04] This is snippy 4.6.0 [07:08:04] Written by Torsten Seemann [07:08:04] Obtained from https://github.com/tseemann/snippy [07:08:04] Detected operating system: linux [07:08:04] Enabling bundled linux tools. [07:08:04] Found bwa - /usr/local/bin/bwa [07:08:04] Found bcftools - /usr/local/bin/bcftools [07:08:04] Found samtools - /usr/local/bin/samtools [07:08:04] Found java - /usr/local/bin/java [07:08:04] Found snpEff - /usr/local/bin/snpEff [07:08:04] Found samclip - /usr/local/bin/samclip [07:08:04] Found seqtk - /usr/local/bin/seqtk [07:08:04] Found parallel - /usr/local/bin/parallel [07:08:04] Found freebayes - /usr/local/bin/freebayes [07:08:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:08:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:08:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:08:04] Found vcfuniq - /usr/local/bin/vcfuniq [07:08:04] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:08:04] Found gzip - /bin/gzip [07:08:04] Found vt - /usr/local/bin/vt [07:08:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:08:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:08:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:08:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:08:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:08:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:08:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:08:05] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:08:25] This is snippy 4.6.0
Show full stderr[07:08:25] This is snippy 4.6.0 [07:08:25] Written by Torsten Seemann [07:08:25] Obtained from https://github.com/tseemann/snippy [07:08:25] Detected operating system: linux [07:08:25] Enabling bundled linux tools. [07:08:25] Found bwa - /usr/local/bin/bwa [07:08:25] Found bcftools - /usr/local/bin/bcftools [07:08:25] Found samtools - /usr/local/bin/samtools [07:08:25] Found java - /usr/local/bin/java [07:08:25] Found snpEff - /usr/local/bin/snpEff [07:08:25] Found samclip - /usr/local/bin/samclip [07:08:25] Found seqtk - /usr/local/bin/seqtk [07:08:25] Found parallel - /usr/local/bin/parallel [07:08:25] Found freebayes - /usr/local/bin/freebayes [07:08:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:08:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:08:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:08:25] Found vcfuniq - /usr/local/bin/vcfuniq [07:08:25] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:08:25] Found gzip - /bin/gzip [07:08:25] Found vt - /usr/local/bin/vt [07:08:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:08:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:08:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:08:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:08:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:08:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:08:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:08:26] Please supply a reference FASTA/GBK/EMBL file with --reference
1[08:22:41] This is snippy 4.6.0
Show full stderr[08:22:41] This is snippy 4.6.0 [08:22:41] Written by Torsten Seemann [08:22:41] Obtained from https://github.com/tseemann/snippy [08:22:41] Detected operating system: linux [08:22:41] Enabling bundled linux tools. [08:22:41] Found bwa - /usr/local/bin/bwa [08:22:41] Found bcftools - /usr/local/bin/bcftools [08:22:41] Found samtools - /usr/local/bin/samtools [08:22:41] Found java - /usr/local/bin/java [08:22:41] Found snpEff - /usr/local/bin/snpEff [08:22:41] Found samclip - /usr/local/bin/samclip [08:22:41] Found seqtk - /usr/local/bin/seqtk [08:22:41] Found parallel - /usr/local/bin/parallel [08:22:41] Found freebayes - /usr/local/bin/freebayes [08:22:41] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:22:41] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:22:41] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:22:41] Found vcfuniq - /usr/local/bin/vcfuniq [08:22:41] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:22:41] Found gzip - /bin/gzip [08:22:41] Found vt - /usr/local/bin/vt [08:22:41] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:22:41] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:22:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:22:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:22:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:22:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:22:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:22:41] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:08:51] This is snippy 4.6.0
Show full stderr[07:08:51] This is snippy 4.6.0 [07:08:51] Written by Torsten Seemann [07:08:51] Obtained from https://github.com/tseemann/snippy [07:08:51] Detected operating system: linux [07:08:51] Enabling bundled linux tools. [07:08:51] Found bwa - /usr/local/bin/bwa [07:08:51] Found bcftools - /usr/local/bin/bcftools [07:08:51] Found samtools - /usr/local/bin/samtools [07:08:51] Found java - /usr/local/bin/java [07:08:51] Found snpEff - /usr/local/bin/snpEff [07:08:51] Found samclip - /usr/local/bin/samclip [07:08:51] Found seqtk - /usr/local/bin/seqtk [07:08:51] Found parallel - /usr/local/bin/parallel [07:08:51] Found freebayes - /usr/local/bin/freebayes [07:08:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:08:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:08:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:08:51] Found vcfuniq - /usr/local/bin/vcfuniq [07:08:51] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:08:51] Found gzip - /bin/gzip [07:08:51] Found vt - /usr/local/bin/vt [07:08:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:08:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:08:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:08:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:08:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:08:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:08:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:08:52] Please supply a reference FASTA/GBK/EMBL file with --reference
1[08:27:35] This is snippy 4.6.0
Show full stderr[08:27:35] This is snippy 4.6.0 [08:27:35] Written by Torsten Seemann [08:27:35] Obtained from https://github.com/tseemann/snippy [08:27:35] Detected operating system: linux [08:27:35] Enabling bundled linux tools. [08:27:35] Found bwa - /usr/local/bin/bwa [08:27:35] Found bcftools - /usr/local/bin/bcftools [08:27:35] Found samtools - /usr/local/bin/samtools [08:27:35] Found java - /usr/local/bin/java [08:27:35] Found snpEff - /usr/local/bin/snpEff [08:27:35] Found samclip - /usr/local/bin/samclip [08:27:35] Found seqtk - /usr/local/bin/seqtk [08:27:35] Found parallel - /usr/local/bin/parallel [08:27:35] Found freebayes - /usr/local/bin/freebayes [08:27:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:27:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:27:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:27:35] Found vcfuniq - /usr/local/bin/vcfuniq [08:27:35] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:27:35] Found gzip - /bin/gzip [08:27:35] Found vt - /usr/local/bin/vt [08:27:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:27:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:27:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:27:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:27:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:27:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:27:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:27:36] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:44:15] This is snippy 4.6.0
Show full stderr[07:44:15] This is snippy 4.6.0 [07:44:15] Written by Torsten Seemann [07:44:15] Obtained from https://github.com/tseemann/snippy [07:44:15] Detected operating system: linux [07:44:15] Enabling bundled linux tools. [07:44:15] Found bwa - /usr/local/bin/bwa [07:44:15] Found bcftools - /usr/local/bin/bcftools [07:44:15] Found samtools - /usr/local/bin/samtools [07:44:15] Found java - /usr/local/bin/java [07:44:15] Found snpEff - /usr/local/bin/snpEff [07:44:15] Found samclip - /usr/local/bin/samclip [07:44:15] Found seqtk - /usr/local/bin/seqtk [07:44:15] Found parallel - /usr/local/bin/parallel [07:44:15] Found freebayes - /usr/local/bin/freebayes [07:44:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:44:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:44:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:44:15] Found vcfuniq - /usr/local/bin/vcfuniq [07:44:15] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:44:15] Found gzip - /bin/gzip [07:44:15] Found vt - /usr/local/bin/vt [07:44:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:44:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:44:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:44:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:44:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:44:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:44:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:44:15] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:44:53] This is snippy 4.6.0
Show full stderr[07:44:53] This is snippy 4.6.0 [07:44:53] Written by Torsten Seemann [07:44:53] Obtained from https://github.com/tseemann/snippy [07:44:53] Detected operating system: linux [07:44:53] Enabling bundled linux tools. [07:44:53] Found bwa - /usr/local/bin/bwa [07:44:53] Found bcftools - /usr/local/bin/bcftools [07:44:53] Found samtools - /usr/local/bin/samtools [07:44:53] Found java - /usr/local/bin/java [07:44:53] Found snpEff - /usr/local/bin/snpEff [07:44:53] Found samclip - /usr/local/bin/samclip [07:44:53] Found seqtk - /usr/local/bin/seqtk [07:44:53] Found parallel - /usr/local/bin/parallel [07:44:53] Found freebayes - /usr/local/bin/freebayes [07:44:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:44:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:44:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:44:53] Found vcfuniq - /usr/local/bin/vcfuniq [07:44:53] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:44:53] Found gzip - /bin/gzip [07:44:53] Found vt - /usr/local/bin/vt [07:44:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:44:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:44:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:44:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:44:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:44:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:44:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:44:54] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:50:27] This is snippy 4.6.0
Show full stderr[07:50:27] This is snippy 4.6.0 [07:50:27] Written by Torsten Seemann [07:50:27] Obtained from https://github.com/tseemann/snippy [07:50:27] Detected operating system: linux [07:50:27] Enabling bundled linux tools. [07:50:27] Found bwa - /usr/local/bin/bwa [07:50:27] Found bcftools - /usr/local/bin/bcftools [07:50:27] Found samtools - /usr/local/bin/samtools [07:50:27] Found java - /usr/local/bin/java [07:50:27] Found snpEff - /usr/local/bin/snpEff [07:50:27] Found samclip - /usr/local/bin/samclip [07:50:27] Found seqtk - /usr/local/bin/seqtk [07:50:27] Found parallel - /usr/local/bin/parallel [07:50:27] Found freebayes - /usr/local/bin/freebayes [07:50:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:50:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:50:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:50:27] Found vcfuniq - /usr/local/bin/vcfuniq [07:50:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:50:27] Found gzip - /bin/gzip [07:50:27] Found vt - /usr/local/bin/vt [07:50:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:50:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:50:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:50:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:50:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:50:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:50:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:50:27] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:57:10] This is snippy 4.6.0
Show full stderr[07:57:10] This is snippy 4.6.0 [07:57:10] Written by Torsten Seemann [07:57:10] Obtained from https://github.com/tseemann/snippy [07:57:10] Detected operating system: linux [07:57:10] Enabling bundled linux tools. [07:57:10] Found bwa - /usr/local/bin/bwa [07:57:10] Found bcftools - /usr/local/bin/bcftools [07:57:10] Found samtools - /usr/local/bin/samtools [07:57:10] Found java - /usr/local/bin/java [07:57:10] Found snpEff - /usr/local/bin/snpEff [07:57:10] Found samclip - /usr/local/bin/samclip [07:57:10] Found seqtk - /usr/local/bin/seqtk [07:57:10] Found parallel - /usr/local/bin/parallel [07:57:10] Found freebayes - /usr/local/bin/freebayes [07:57:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:57:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:57:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:57:10] Found vcfuniq - /usr/local/bin/vcfuniq [07:57:10] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:57:10] Found gzip - /bin/gzip [07:57:10] Found vt - /usr/local/bin/vt [07:57:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:57:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:57:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:57:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:57:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:57:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:57:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:57:11] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:57:12] This is snippy 4.6.0
Show full stderr[07:57:12] This is snippy 4.6.0 [07:57:12] Written by Torsten Seemann [07:57:12] Obtained from https://github.com/tseemann/snippy [07:57:12] Detected operating system: linux [07:57:12] Enabling bundled linux tools. [07:57:12] Found bwa - /usr/local/bin/bwa [07:57:12] Found bcftools - /usr/local/bin/bcftools [07:57:12] Found samtools - /usr/local/bin/samtools [07:57:12] Found java - /usr/local/bin/java [07:57:12] Found snpEff - /usr/local/bin/snpEff [07:57:12] Found samclip - /usr/local/bin/samclip [07:57:12] Found seqtk - /usr/local/bin/seqtk [07:57:12] Found parallel - /usr/local/bin/parallel [07:57:12] Found freebayes - /usr/local/bin/freebayes [07:57:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:57:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:57:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:57:12] Found vcfuniq - /usr/local/bin/vcfuniq [07:57:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:57:12] Found gzip - /bin/gzip [07:57:12] Found vt - /usr/local/bin/vt [07:57:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:57:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:57:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:57:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:57:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:57:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:57:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:57:13] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:57:27] This is snippy 4.6.0
Show full stderr[07:57:27] This is snippy 4.6.0 [07:57:27] Written by Torsten Seemann [07:57:27] Obtained from https://github.com/tseemann/snippy [07:57:27] Detected operating system: linux [07:57:27] Enabling bundled linux tools. [07:57:27] Found bwa - /usr/local/bin/bwa [07:57:27] Found bcftools - /usr/local/bin/bcftools [07:57:27] Found samtools - /usr/local/bin/samtools [07:57:27] Found java - /usr/local/bin/java [07:57:27] Found snpEff - /usr/local/bin/snpEff [07:57:27] Found samclip - /usr/local/bin/samclip [07:57:27] Found seqtk - /usr/local/bin/seqtk [07:57:27] Found parallel - /usr/local/bin/parallel [07:57:27] Found freebayes - /usr/local/bin/freebayes [07:57:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:57:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:57:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:57:27] Found vcfuniq - /usr/local/bin/vcfuniq [07:57:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:57:27] Found gzip - /bin/gzip [07:57:27] Found vt - /usr/local/bin/vt [07:57:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:57:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:57:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:57:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:57:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:57:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:57:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:57:28] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:57:30] This is snippy 4.6.0
Show full stderr[07:57:30] This is snippy 4.6.0 [07:57:30] Written by Torsten Seemann [07:57:30] Obtained from https://github.com/tseemann/snippy [07:57:30] Detected operating system: linux [07:57:30] Enabling bundled linux tools. [07:57:30] Found bwa - /usr/local/bin/bwa [07:57:30] Found bcftools - /usr/local/bin/bcftools [07:57:30] Found samtools - /usr/local/bin/samtools [07:57:30] Found java - /usr/local/bin/java [07:57:30] Found snpEff - /usr/local/bin/snpEff [07:57:30] Found samclip - /usr/local/bin/samclip [07:57:30] Found seqtk - /usr/local/bin/seqtk [07:57:30] Found parallel - /usr/local/bin/parallel [07:57:30] Found freebayes - /usr/local/bin/freebayes [07:57:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:57:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:57:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:57:30] Found vcfuniq - /usr/local/bin/vcfuniq [07:57:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:57:30] Found gzip - /bin/gzip [07:57:30] Found vt - /usr/local/bin/vt [07:57:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:57:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:57:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:57:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:57:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:57:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:57:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:57:31] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:04:49] This is snippy 4.6.0
Show full stderr[07:04:49] This is snippy 4.6.0 [07:04:49] Written by Torsten Seemann [07:04:49] Obtained from https://github.com/tseemann/snippy [07:04:49] Detected operating system: linux [07:04:49] Enabling bundled linux tools. [07:04:49] Found bwa - /usr/local/bin/bwa [07:04:49] Found bcftools - /usr/local/bin/bcftools [07:04:49] Found samtools - /usr/local/bin/samtools [07:04:49] Found java - /usr/local/bin/java [07:04:49] Found snpEff - /usr/local/bin/snpEff [07:04:49] Found samclip - /usr/local/bin/samclip [07:04:49] Found seqtk - /usr/local/bin/seqtk [07:04:49] Found parallel - /usr/local/bin/parallel [07:04:49] Found freebayes - /usr/local/bin/freebayes [07:04:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:04:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:04:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:04:49] Found vcfuniq - /usr/local/bin/vcfuniq [07:04:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:04:49] Found gzip - /bin/gzip [07:04:49] Found vt - /usr/local/bin/vt [07:04:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:04:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:04:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:04:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:04:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:04:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:04:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:04:50] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:04:55] This is snippy 4.6.0
Show full stderr[07:04:55] This is snippy 4.6.0 [07:04:55] Written by Torsten Seemann [07:04:55] Obtained from https://github.com/tseemann/snippy [07:04:55] Detected operating system: linux [07:04:55] Enabling bundled linux tools. [07:04:55] Found bwa - /usr/local/bin/bwa [07:04:55] Found bcftools - /usr/local/bin/bcftools [07:04:55] Found samtools - /usr/local/bin/samtools [07:04:55] Found java - /usr/local/bin/java [07:04:55] Found snpEff - /usr/local/bin/snpEff [07:04:55] Found samclip - /usr/local/bin/samclip [07:04:55] Found seqtk - /usr/local/bin/seqtk [07:04:55] Found parallel - /usr/local/bin/parallel [07:04:55] Found freebayes - /usr/local/bin/freebayes [07:04:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:04:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:04:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:04:55] Found vcfuniq - /usr/local/bin/vcfuniq [07:04:55] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:04:55] Found gzip - /bin/gzip [07:04:55] Found vt - /usr/local/bin/vt [07:04:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:04:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:04:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:04:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:04:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:04:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:04:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:04:56] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:04:58] This is snippy 4.6.0
Show full stderr[07:04:58] This is snippy 4.6.0 [07:04:58] Written by Torsten Seemann [07:04:58] Obtained from https://github.com/tseemann/snippy [07:04:58] Detected operating system: linux [07:04:58] Enabling bundled linux tools. [07:04:58] Found bwa - /usr/local/bin/bwa [07:04:58] Found bcftools - /usr/local/bin/bcftools [07:04:58] Found samtools - /usr/local/bin/samtools [07:04:58] Found java - /usr/local/bin/java [07:04:58] Found snpEff - /usr/local/bin/snpEff [07:04:58] Found samclip - /usr/local/bin/samclip [07:04:58] Found seqtk - /usr/local/bin/seqtk [07:04:58] Found parallel - /usr/local/bin/parallel [07:04:58] Found freebayes - /usr/local/bin/freebayes [07:04:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:04:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:04:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:04:58] Found vcfuniq - /usr/local/bin/vcfuniq [07:04:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:04:58] Found gzip - /bin/gzip [07:04:58] Found vt - /usr/local/bin/vt [07:04:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:04:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:04:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:04:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:04:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:04:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:04:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:04:59] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:05:10] This is snippy 4.6.0
Show full stderr[07:05:10] This is snippy 4.6.0 [07:05:10] Written by Torsten Seemann [07:05:10] Obtained from https://github.com/tseemann/snippy [07:05:10] Detected operating system: linux [07:05:10] Enabling bundled linux tools. [07:05:10] Found bwa - /usr/local/bin/bwa [07:05:10] Found bcftools - /usr/local/bin/bcftools [07:05:10] Found samtools - /usr/local/bin/samtools [07:05:10] Found java - /usr/local/bin/java [07:05:10] Found snpEff - /usr/local/bin/snpEff [07:05:10] Found samclip - /usr/local/bin/samclip [07:05:10] Found seqtk - /usr/local/bin/seqtk [07:05:10] Found parallel - /usr/local/bin/parallel [07:05:10] Found freebayes - /usr/local/bin/freebayes [07:05:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:05:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:05:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:05:10] Found vcfuniq - /usr/local/bin/vcfuniq [07:05:10] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:05:10] Found gzip - /bin/gzip [07:05:10] Found vt - /usr/local/bin/vt [07:05:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:05:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:05:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:05:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:05:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:05:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:05:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:05:11] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:05:23] This is snippy 4.6.0
Show full stderr[07:05:23] This is snippy 4.6.0 [07:05:23] Written by Torsten Seemann [07:05:23] Obtained from https://github.com/tseemann/snippy [07:05:23] Detected operating system: linux [07:05:23] Enabling bundled linux tools. [07:05:23] Found bwa - /usr/local/bin/bwa [07:05:23] Found bcftools - /usr/local/bin/bcftools [07:05:23] Found samtools - /usr/local/bin/samtools [07:05:23] Found java - /usr/local/bin/java [07:05:23] Found snpEff - /usr/local/bin/snpEff [07:05:23] Found samclip - /usr/local/bin/samclip [07:05:23] Found seqtk - /usr/local/bin/seqtk [07:05:23] Found parallel - /usr/local/bin/parallel [07:05:23] Found freebayes - /usr/local/bin/freebayes [07:05:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:05:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:05:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:05:23] Found vcfuniq - /usr/local/bin/vcfuniq [07:05:23] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:05:23] Found gzip - /bin/gzip [07:05:23] Found vt - /usr/local/bin/vt [07:05:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:05:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:05:23] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:05:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:05:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:05:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:05:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:05:24] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:06:22] This is snippy 4.6.0
Show full stderr[07:06:22] This is snippy 4.6.0 [07:06:22] Written by Torsten Seemann [07:06:22] Obtained from https://github.com/tseemann/snippy [07:06:22] Detected operating system: linux [07:06:22] Enabling bundled linux tools. [07:06:22] Found bwa - /usr/local/bin/bwa [07:06:22] Found bcftools - /usr/local/bin/bcftools [07:06:22] Found samtools - /usr/local/bin/samtools [07:06:22] Found java - /usr/local/bin/java [07:06:22] Found snpEff - /usr/local/bin/snpEff [07:06:22] Found samclip - /usr/local/bin/samclip [07:06:22] Found seqtk - /usr/local/bin/seqtk [07:06:22] Found parallel - /usr/local/bin/parallel [07:06:22] Found freebayes - /usr/local/bin/freebayes [07:06:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:06:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:06:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:06:22] Found vcfuniq - /usr/local/bin/vcfuniq [07:06:22] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:06:22] Found gzip - /bin/gzip [07:06:22] Found vt - /usr/local/bin/vt [07:06:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:06:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:06:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:06:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:06:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:06:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:06:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:06:23] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:06:50] This is snippy 4.6.0
Show full stderr[07:06:50] This is snippy 4.6.0 [07:06:50] Written by Torsten Seemann [07:06:50] Obtained from https://github.com/tseemann/snippy [07:06:50] Detected operating system: linux [07:06:50] Enabling bundled linux tools. [07:06:50] Found bwa - /usr/local/bin/bwa [07:06:50] Found bcftools - /usr/local/bin/bcftools [07:06:50] Found samtools - /usr/local/bin/samtools [07:06:50] Found java - /usr/local/bin/java [07:06:50] Found snpEff - /usr/local/bin/snpEff [07:06:50] Found samclip - /usr/local/bin/samclip [07:06:50] Found seqtk - /usr/local/bin/seqtk [07:06:50] Found parallel - /usr/local/bin/parallel [07:06:50] Found freebayes - /usr/local/bin/freebayes [07:06:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:06:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:06:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:06:50] Found vcfuniq - /usr/local/bin/vcfuniq [07:06:50] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:06:50] Found gzip - /bin/gzip [07:06:50] Found vt - /usr/local/bin/vt [07:06:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:06:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:06:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:06:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:06:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:06:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:06:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:06:51] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:07:47] This is snippy 4.6.0
Show full stderr[07:07:47] This is snippy 4.6.0 [07:07:47] Written by Torsten Seemann [07:07:47] Obtained from https://github.com/tseemann/snippy [07:07:47] Detected operating system: linux [07:07:47] Enabling bundled linux tools. [07:07:47] Found bwa - /usr/local/bin/bwa [07:07:47] Found bcftools - /usr/local/bin/bcftools [07:07:47] Found samtools - /usr/local/bin/samtools [07:07:47] Found java - /usr/local/bin/java [07:07:47] Found snpEff - /usr/local/bin/snpEff [07:07:47] Found samclip - /usr/local/bin/samclip [07:07:47] Found seqtk - /usr/local/bin/seqtk [07:07:47] Found parallel - /usr/local/bin/parallel [07:07:47] Found freebayes - /usr/local/bin/freebayes [07:07:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:07:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:07:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:07:47] Found vcfuniq - /usr/local/bin/vcfuniq [07:07:47] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:07:47] Found gzip - /bin/gzip [07:07:47] Found vt - /usr/local/bin/vt [07:07:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:07:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:07:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:07:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:07:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:07:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:07:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:07:48] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:07:53] This is snippy 4.6.0
Show full stderr[07:07:53] This is snippy 4.6.0 [07:07:53] Written by Torsten Seemann [07:07:53] Obtained from https://github.com/tseemann/snippy [07:07:53] Detected operating system: linux [07:07:53] Enabling bundled linux tools. [07:07:53] Found bwa - /usr/local/bin/bwa [07:07:53] Found bcftools - /usr/local/bin/bcftools [07:07:53] Found samtools - /usr/local/bin/samtools [07:07:53] Found java - /usr/local/bin/java [07:07:53] Found snpEff - /usr/local/bin/snpEff [07:07:53] Found samclip - /usr/local/bin/samclip [07:07:53] Found seqtk - /usr/local/bin/seqtk [07:07:53] Found parallel - /usr/local/bin/parallel [07:07:53] Found freebayes - /usr/local/bin/freebayes [07:07:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:07:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:07:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:07:53] Found vcfuniq - /usr/local/bin/vcfuniq [07:07:53] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:07:53] Found gzip - /bin/gzip [07:07:53] Found vt - /usr/local/bin/vt [07:07:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:07:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:07:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:07:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:07:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:07:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:07:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:07:54] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:08:02] This is snippy 4.6.0
Show full stderr[07:08:02] This is snippy 4.6.0 [07:08:02] Written by Torsten Seemann [07:08:02] Obtained from https://github.com/tseemann/snippy [07:08:02] Detected operating system: linux [07:08:02] Enabling bundled linux tools. [07:08:02] Found bwa - /usr/local/bin/bwa [07:08:02] Found bcftools - /usr/local/bin/bcftools [07:08:02] Found samtools - /usr/local/bin/samtools [07:08:02] Found java - /usr/local/bin/java [07:08:02] Found snpEff - /usr/local/bin/snpEff [07:08:02] Found samclip - /usr/local/bin/samclip [07:08:02] Found seqtk - /usr/local/bin/seqtk [07:08:02] Found parallel - /usr/local/bin/parallel [07:08:02] Found freebayes - /usr/local/bin/freebayes [07:08:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:08:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:08:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:08:02] Found vcfuniq - /usr/local/bin/vcfuniq [07:08:02] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:08:02] Found gzip - /bin/gzip [07:08:02] Found vt - /usr/local/bin/vt [07:08:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:08:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:08:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:08:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:08:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:08:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:08:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:08:03] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:08:37] This is snippy 4.6.0
Show full stderr[07:08:37] This is snippy 4.6.0 [07:08:37] Written by Torsten Seemann [07:08:37] Obtained from https://github.com/tseemann/snippy [07:08:37] Detected operating system: linux [07:08:37] Enabling bundled linux tools. [07:08:37] Found bwa - /usr/local/bin/bwa [07:08:37] Found bcftools - /usr/local/bin/bcftools [07:08:37] Found samtools - /usr/local/bin/samtools [07:08:37] Found java - /usr/local/bin/java [07:08:37] Found snpEff - /usr/local/bin/snpEff [07:08:37] Found samclip - /usr/local/bin/samclip [07:08:37] Found seqtk - /usr/local/bin/seqtk [07:08:37] Found parallel - /usr/local/bin/parallel [07:08:37] Found freebayes - /usr/local/bin/freebayes [07:08:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:08:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:08:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:08:37] Found vcfuniq - /usr/local/bin/vcfuniq [07:08:37] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:08:37] Found gzip - /bin/gzip [07:08:37] Found vt - /usr/local/bin/vt [07:08:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:08:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:08:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:08:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:08:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:08:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:08:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:08:38] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:08:48] This is snippy 4.6.0
Show full stderr[07:08:48] This is snippy 4.6.0 [07:08:48] Written by Torsten Seemann [07:08:48] Obtained from https://github.com/tseemann/snippy [07:08:48] Detected operating system: linux [07:08:48] Enabling bundled linux tools. [07:08:48] Found bwa - /usr/local/bin/bwa [07:08:48] Found bcftools - /usr/local/bin/bcftools [07:08:48] Found samtools - /usr/local/bin/samtools [07:08:48] Found java - /usr/local/bin/java [07:08:48] Found snpEff - /usr/local/bin/snpEff [07:08:48] Found samclip - /usr/local/bin/samclip [07:08:48] Found seqtk - /usr/local/bin/seqtk [07:08:48] Found parallel - /usr/local/bin/parallel [07:08:48] Found freebayes - /usr/local/bin/freebayes [07:08:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:08:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:08:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:08:48] Found vcfuniq - /usr/local/bin/vcfuniq [07:08:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:08:48] Found gzip - /bin/gzip [07:08:48] Found vt - /usr/local/bin/vt [07:08:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:08:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:08:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:08:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:08:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:08:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:08:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:08:49] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:09:00] This is snippy 4.6.0
Show full stderr[07:09:00] This is snippy 4.6.0 [07:09:00] Written by Torsten Seemann [07:09:00] Obtained from https://github.com/tseemann/snippy [07:09:00] Detected operating system: linux [07:09:00] Enabling bundled linux tools. [07:09:00] Found bwa - /usr/local/bin/bwa [07:09:00] Found bcftools - /usr/local/bin/bcftools [07:09:00] Found samtools - /usr/local/bin/samtools [07:09:00] Found java - /usr/local/bin/java [07:09:00] Found snpEff - /usr/local/bin/snpEff [07:09:00] Found samclip - /usr/local/bin/samclip [07:09:00] Found seqtk - /usr/local/bin/seqtk [07:09:00] Found parallel - /usr/local/bin/parallel [07:09:00] Found freebayes - /usr/local/bin/freebayes [07:09:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:09:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:09:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:09:00] Found vcfuniq - /usr/local/bin/vcfuniq [07:09:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:09:00] Found gzip - /bin/gzip [07:09:00] Found vt - /usr/local/bin/vt [07:09:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:09:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:09:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:09:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:09:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:09:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:09:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:09:01] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:15:41] This is snippy 4.6.0
Show full stderr[07:15:41] This is snippy 4.6.0 [07:15:41] Written by Torsten Seemann [07:15:41] Obtained from https://github.com/tseemann/snippy [07:15:41] Detected operating system: linux [07:15:41] Enabling bundled linux tools. [07:15:41] Found bwa - /usr/local/bin/bwa [07:15:41] Found bcftools - /usr/local/bin/bcftools [07:15:41] Found samtools - /usr/local/bin/samtools [07:15:41] Found java - /usr/local/bin/java [07:15:41] Found snpEff - /usr/local/bin/snpEff [07:15:41] Found samclip - /usr/local/bin/samclip [07:15:41] Found seqtk - /usr/local/bin/seqtk [07:15:41] Found parallel - /usr/local/bin/parallel [07:15:41] Found freebayes - /usr/local/bin/freebayes [07:15:41] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:15:41] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:15:41] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:15:41] Found vcfuniq - /usr/local/bin/vcfuniq [07:15:41] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:15:41] Found gzip - /bin/gzip [07:15:41] Found vt - /usr/local/bin/vt [07:15:41] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:15:41] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:15:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:15:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:15:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:15:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:15:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:15:42] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:07:41] This is snippy 4.6.0
Show full stderr[07:07:41] This is snippy 4.6.0 [07:07:41] Written by Torsten Seemann [07:07:41] Obtained from https://github.com/tseemann/snippy [07:07:41] Detected operating system: linux [07:07:41] Enabling bundled linux tools. [07:07:41] Found bwa - /usr/local/bin/bwa [07:07:41] Found bcftools - /usr/local/bin/bcftools [07:07:41] Found samtools - /usr/local/bin/samtools [07:07:41] Found java - /usr/local/bin/java [07:07:41] Found snpEff - /usr/local/bin/snpEff [07:07:41] Found samclip - /usr/local/bin/samclip [07:07:41] Found seqtk - /usr/local/bin/seqtk [07:07:41] Found parallel - /usr/local/bin/parallel [07:07:41] Found freebayes - /usr/local/bin/freebayes [07:07:41] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:07:41] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:07:41] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:07:41] Found vcfuniq - /usr/local/bin/vcfuniq [07:07:41] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:07:41] Found gzip - /bin/gzip [07:07:41] Found vt - /usr/local/bin/vt [07:07:41] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:07:41] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:07:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:07:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:07:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:07:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:07:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:07:42] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:08:07] This is snippy 4.6.0
Show full stderr[07:08:07] This is snippy 4.6.0 [07:08:07] Written by Torsten Seemann [07:08:07] Obtained from https://github.com/tseemann/snippy [07:08:07] Detected operating system: linux [07:08:07] Enabling bundled linux tools. [07:08:07] Found bwa - /usr/local/bin/bwa [07:08:07] Found bcftools - /usr/local/bin/bcftools [07:08:07] Found samtools - /usr/local/bin/samtools [07:08:07] Found java - /usr/local/bin/java [07:08:07] Found snpEff - /usr/local/bin/snpEff [07:08:07] Found samclip - /usr/local/bin/samclip [07:08:07] Found seqtk - /usr/local/bin/seqtk [07:08:07] Found parallel - /usr/local/bin/parallel [07:08:07] Found freebayes - /usr/local/bin/freebayes [07:08:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:08:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:08:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:08:07] Found vcfuniq - /usr/local/bin/vcfuniq [07:08:07] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:08:07] Found gzip - /bin/gzip [07:08:07] Found vt - /usr/local/bin/vt [07:08:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:08:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:08:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:08:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:08:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:08:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:08:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:08:08] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:08:10] This is snippy 4.6.0
Show full stderr[07:08:10] This is snippy 4.6.0 [07:08:10] Written by Torsten Seemann [07:08:10] Obtained from https://github.com/tseemann/snippy [07:08:10] Detected operating system: linux [07:08:10] Enabling bundled linux tools. [07:08:10] Found bwa - /usr/local/bin/bwa [07:08:10] Found bcftools - /usr/local/bin/bcftools [07:08:10] Found samtools - /usr/local/bin/samtools [07:08:10] Found java - /usr/local/bin/java [07:08:10] Found snpEff - /usr/local/bin/snpEff [07:08:10] Found samclip - /usr/local/bin/samclip [07:08:10] Found seqtk - /usr/local/bin/seqtk [07:08:10] Found parallel - /usr/local/bin/parallel [07:08:10] Found freebayes - /usr/local/bin/freebayes [07:08:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:08:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:08:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:08:10] Found vcfuniq - /usr/local/bin/vcfuniq [07:08:10] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:08:10] Found gzip - /bin/gzip [07:08:10] Found vt - /usr/local/bin/vt [07:08:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:08:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:08:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:08:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:08:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:08:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:08:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:08:11] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:09:03] This is snippy 4.6.0
Show full stderr[07:09:03] This is snippy 4.6.0 [07:09:03] Written by Torsten Seemann [07:09:03] Obtained from https://github.com/tseemann/snippy [07:09:03] Detected operating system: linux [07:09:03] Enabling bundled linux tools. [07:09:03] Found bwa - /usr/local/bin/bwa [07:09:03] Found bcftools - /usr/local/bin/bcftools [07:09:03] Found samtools - /usr/local/bin/samtools [07:09:03] Found java - /usr/local/bin/java [07:09:03] Found snpEff - /usr/local/bin/snpEff [07:09:03] Found samclip - /usr/local/bin/samclip [07:09:03] Found seqtk - /usr/local/bin/seqtk [07:09:03] Found parallel - /usr/local/bin/parallel [07:09:03] Found freebayes - /usr/local/bin/freebayes [07:09:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:09:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:09:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:09:03] Found vcfuniq - /usr/local/bin/vcfuniq [07:09:03] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:09:03] Found gzip - /bin/gzip [07:09:03] Found vt - /usr/local/bin/vt [07:09:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:09:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:09:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:09:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:09:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:09:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:09:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:09:04] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:09:23] This is snippy 4.6.0
Show full stderr[07:09:23] This is snippy 4.6.0 [07:09:23] Written by Torsten Seemann [07:09:23] Obtained from https://github.com/tseemann/snippy [07:09:23] Detected operating system: linux [07:09:23] Enabling bundled linux tools. [07:09:23] Found bwa - /usr/local/bin/bwa [07:09:23] Found bcftools - /usr/local/bin/bcftools [07:09:23] Found samtools - /usr/local/bin/samtools [07:09:23] Found java - /usr/local/bin/java [07:09:23] Found snpEff - /usr/local/bin/snpEff [07:09:23] Found samclip - /usr/local/bin/samclip [07:09:23] Found seqtk - /usr/local/bin/seqtk [07:09:23] Found parallel - /usr/local/bin/parallel [07:09:23] Found freebayes - /usr/local/bin/freebayes [07:09:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:09:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:09:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:09:23] Found vcfuniq - /usr/local/bin/vcfuniq [07:09:23] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:09:23] Found gzip - /bin/gzip [07:09:23] Found vt - /usr/local/bin/vt [07:09:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:09:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:09:23] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:09:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:09:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:09:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:09:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:09:24] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:09:29] This is snippy 4.6.0
Show full stderr[07:09:29] This is snippy 4.6.0 [07:09:29] Written by Torsten Seemann [07:09:29] Obtained from https://github.com/tseemann/snippy [07:09:29] Detected operating system: linux [07:09:29] Enabling bundled linux tools. [07:09:29] Found bwa - /usr/local/bin/bwa [07:09:29] Found bcftools - /usr/local/bin/bcftools [07:09:29] Found samtools - /usr/local/bin/samtools [07:09:29] Found java - /usr/local/bin/java [07:09:29] Found snpEff - /usr/local/bin/snpEff [07:09:29] Found samclip - /usr/local/bin/samclip [07:09:29] Found seqtk - /usr/local/bin/seqtk [07:09:29] Found parallel - /usr/local/bin/parallel [07:09:29] Found freebayes - /usr/local/bin/freebayes [07:09:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:09:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:09:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:09:29] Found vcfuniq - /usr/local/bin/vcfuniq [07:09:29] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:09:29] Found gzip - /bin/gzip [07:09:29] Found vt - /usr/local/bin/vt [07:09:29] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:09:29] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:09:29] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:09:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:09:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:09:30] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:09:30] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:09:30] Please supply a reference FASTA/GBK/EMBL file with --reference
1[08:03:13] This is snippy 4.6.0
Show full stderr[08:03:13] This is snippy 4.6.0 [08:03:13] Written by Torsten Seemann [08:03:13] Obtained from https://github.com/tseemann/snippy [08:03:13] Detected operating system: linux [08:03:13] Enabling bundled linux tools. [08:03:13] Found bwa - /usr/local/bin/bwa [08:03:13] Found bcftools - /usr/local/bin/bcftools [08:03:13] Found samtools - /usr/local/bin/samtools [08:03:13] Found java - /usr/local/bin/java [08:03:13] Found snpEff - /usr/local/bin/snpEff [08:03:13] Found samclip - /usr/local/bin/samclip [08:03:13] Found seqtk - /usr/local/bin/seqtk [08:03:13] Found parallel - /usr/local/bin/parallel [08:03:13] Found freebayes - /usr/local/bin/freebayes [08:03:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:03:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:03:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:03:13] Found vcfuniq - /usr/local/bin/vcfuniq [08:03:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:03:13] Found gzip - /bin/gzip [08:03:13] Found vt - /usr/local/bin/vt [08:03:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:03:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:03:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:03:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:03:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:03:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:03:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:03:13] Please supply a reference FASTA/GBK/EMBL file with --reference
1[08:03:26] This is snippy 4.6.0
Show full stderr[08:03:26] This is snippy 4.6.0 [08:03:26] Written by Torsten Seemann [08:03:26] Obtained from https://github.com/tseemann/snippy [08:03:26] Detected operating system: linux [08:03:26] Enabling bundled linux tools. [08:03:26] Found bwa - /usr/local/bin/bwa [08:03:26] Found bcftools - /usr/local/bin/bcftools [08:03:26] Found samtools - /usr/local/bin/samtools [08:03:26] Found java - /usr/local/bin/java [08:03:26] Found snpEff - /usr/local/bin/snpEff [08:03:26] Found samclip - /usr/local/bin/samclip [08:03:26] Found seqtk - /usr/local/bin/seqtk [08:03:26] Found parallel - /usr/local/bin/parallel [08:03:26] Found freebayes - /usr/local/bin/freebayes [08:03:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:03:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:03:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:03:26] Found vcfuniq - /usr/local/bin/vcfuniq [08:03:26] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:03:26] Found gzip - /bin/gzip [08:03:26] Found vt - /usr/local/bin/vt [08:03:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:03:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:03:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:03:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:03:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:03:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:03:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:03:26] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:06:35] This is snippy 4.6.0
Show full stderr[07:06:35] This is snippy 4.6.0 [07:06:35] Written by Torsten Seemann [07:06:35] Obtained from https://github.com/tseemann/snippy [07:06:35] Detected operating system: linux [07:06:35] Enabling bundled linux tools. [07:06:35] Found bwa - /usr/local/bin/bwa [07:06:35] Found bcftools - /usr/local/bin/bcftools [07:06:35] Found samtools - /usr/local/bin/samtools [07:06:35] Found java - /usr/local/bin/java [07:06:35] Found snpEff - /usr/local/bin/snpEff [07:06:35] Found samclip - /usr/local/bin/samclip [07:06:35] Found seqtk - /usr/local/bin/seqtk [07:06:35] Found parallel - /usr/local/bin/parallel [07:06:35] Found freebayes - /usr/local/bin/freebayes [07:06:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:06:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:06:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:06:35] Found vcfuniq - /usr/local/bin/vcfuniq [07:06:35] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:06:35] Found gzip - /bin/gzip [07:06:35] Found vt - /usr/local/bin/vt [07:06:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:06:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:06:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:06:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:06:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:06:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:06:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:06:36] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:06:41] This is snippy 4.6.0
Show full stderr[07:06:41] This is snippy 4.6.0 [07:06:41] Written by Torsten Seemann [07:06:41] Obtained from https://github.com/tseemann/snippy [07:06:41] Detected operating system: linux [07:06:41] Enabling bundled linux tools. [07:06:41] Found bwa - /usr/local/bin/bwa [07:06:41] Found bcftools - /usr/local/bin/bcftools [07:06:41] Found samtools - /usr/local/bin/samtools [07:06:41] Found java - /usr/local/bin/java [07:06:41] Found snpEff - /usr/local/bin/snpEff [07:06:41] Found samclip - /usr/local/bin/samclip [07:06:41] Found seqtk - /usr/local/bin/seqtk [07:06:41] Found parallel - /usr/local/bin/parallel [07:06:41] Found freebayes - /usr/local/bin/freebayes [07:06:41] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:06:41] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:06:41] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:06:41] Found vcfuniq - /usr/local/bin/vcfuniq [07:06:41] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:06:41] Found gzip - /bin/gzip [07:06:41] Found vt - /usr/local/bin/vt [07:06:41] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:06:41] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:06:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:06:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:06:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:06:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:06:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:06:42] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:07:25] This is snippy 4.6.0
Show full stderr[07:07:25] This is snippy 4.6.0 [07:07:25] Written by Torsten Seemann [07:07:25] Obtained from https://github.com/tseemann/snippy [07:07:25] Detected operating system: linux [07:07:25] Enabling bundled linux tools. [07:07:25] Found bwa - /usr/local/bin/bwa [07:07:25] Found bcftools - /usr/local/bin/bcftools [07:07:25] Found samtools - /usr/local/bin/samtools [07:07:25] Found java - /usr/local/bin/java [07:07:25] Found snpEff - /usr/local/bin/snpEff [07:07:25] Found samclip - /usr/local/bin/samclip [07:07:25] Found seqtk - /usr/local/bin/seqtk [07:07:25] Found parallel - /usr/local/bin/parallel [07:07:25] Found freebayes - /usr/local/bin/freebayes [07:07:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:07:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:07:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:07:25] Found vcfuniq - /usr/local/bin/vcfuniq [07:07:25] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:07:25] Found gzip - /bin/gzip [07:07:25] Found vt - /usr/local/bin/vt [07:07:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:07:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:07:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:07:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:07:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:07:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:07:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:07:26] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:07:50] This is snippy 4.6.0
Show full stderr[07:07:50] This is snippy 4.6.0 [07:07:50] Written by Torsten Seemann [07:07:50] Obtained from https://github.com/tseemann/snippy [07:07:50] Detected operating system: linux [07:07:50] Enabling bundled linux tools. [07:07:50] Found bwa - /usr/local/bin/bwa [07:07:50] Found bcftools - /usr/local/bin/bcftools [07:07:50] Found samtools - /usr/local/bin/samtools [07:07:50] Found java - /usr/local/bin/java [07:07:50] Found snpEff - /usr/local/bin/snpEff [07:07:50] Found samclip - /usr/local/bin/samclip [07:07:50] Found seqtk - /usr/local/bin/seqtk [07:07:50] Found parallel - /usr/local/bin/parallel [07:07:50] Found freebayes - /usr/local/bin/freebayes [07:07:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:07:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:07:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:07:50] Found vcfuniq - /usr/local/bin/vcfuniq [07:07:50] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:07:50] Found gzip - /bin/gzip [07:07:50] Found vt - /usr/local/bin/vt [07:07:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:07:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:07:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:07:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:07:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:07:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:07:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:07:51] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:08:16] This is snippy 4.6.0
Show full stderr[07:08:16] This is snippy 4.6.0 [07:08:16] Written by Torsten Seemann [07:08:16] Obtained from https://github.com/tseemann/snippy [07:08:16] Detected operating system: linux [07:08:16] Enabling bundled linux tools. [07:08:16] Found bwa - /usr/local/bin/bwa [07:08:16] Found bcftools - /usr/local/bin/bcftools [07:08:16] Found samtools - /usr/local/bin/samtools [07:08:16] Found java - /usr/local/bin/java [07:08:16] Found snpEff - /usr/local/bin/snpEff [07:08:16] Found samclip - /usr/local/bin/samclip [07:08:16] Found seqtk - /usr/local/bin/seqtk [07:08:16] Found parallel - /usr/local/bin/parallel [07:08:16] Found freebayes - /usr/local/bin/freebayes [07:08:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:08:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:08:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:08:16] Found vcfuniq - /usr/local/bin/vcfuniq [07:08:16] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:08:16] Found gzip - /bin/gzip [07:08:16] Found vt - /usr/local/bin/vt [07:08:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:08:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:08:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:08:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:08:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:08:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:08:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:08:17] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:09:14] This is snippy 4.6.0
Show full stderr[07:09:14] This is snippy 4.6.0 [07:09:14] Written by Torsten Seemann [07:09:14] Obtained from https://github.com/tseemann/snippy [07:09:14] Detected operating system: linux [07:09:14] Enabling bundled linux tools. [07:09:14] Found bwa - /usr/local/bin/bwa [07:09:14] Found bcftools - /usr/local/bin/bcftools [07:09:14] Found samtools - /usr/local/bin/samtools [07:09:14] Found java - /usr/local/bin/java [07:09:14] Found snpEff - /usr/local/bin/snpEff [07:09:14] Found samclip - /usr/local/bin/samclip [07:09:14] Found seqtk - /usr/local/bin/seqtk [07:09:14] Found parallel - /usr/local/bin/parallel [07:09:14] Found freebayes - /usr/local/bin/freebayes [07:09:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:09:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:09:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:09:14] Found vcfuniq - /usr/local/bin/vcfuniq [07:09:14] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:09:14] Found gzip - /bin/gzip [07:09:14] Found vt - /usr/local/bin/vt [07:09:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:09:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:09:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:09:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:09:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:09:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:09:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:09:15] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:09:41] This is snippy 4.6.0
Show full stderr[07:09:41] This is snippy 4.6.0 [07:09:41] Written by Torsten Seemann [07:09:41] Obtained from https://github.com/tseemann/snippy [07:09:41] Detected operating system: linux [07:09:41] Enabling bundled linux tools. [07:09:41] Found bwa - /usr/local/bin/bwa [07:09:41] Found bcftools - /usr/local/bin/bcftools [07:09:41] Found samtools - /usr/local/bin/samtools [07:09:41] Found java - /usr/local/bin/java [07:09:41] Found snpEff - /usr/local/bin/snpEff [07:09:41] Found samclip - /usr/local/bin/samclip [07:09:41] Found seqtk - /usr/local/bin/seqtk [07:09:41] Found parallel - /usr/local/bin/parallel [07:09:41] Found freebayes - /usr/local/bin/freebayes [07:09:41] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:09:41] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:09:41] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:09:41] Found vcfuniq - /usr/local/bin/vcfuniq [07:09:41] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:09:41] Found gzip - /bin/gzip [07:09:41] Found vt - /usr/local/bin/vt [07:09:41] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:09:41] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:09:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:09:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:09:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:09:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:09:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:09:42] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:10:54] This is snippy 4.6.0
Show full stderr[07:10:54] This is snippy 4.6.0 [07:10:54] Written by Torsten Seemann [07:10:54] Obtained from https://github.com/tseemann/snippy [07:10:54] Detected operating system: linux [07:10:54] Enabling bundled linux tools. [07:10:54] Found bwa - /usr/local/bin/bwa [07:10:54] Found bcftools - /usr/local/bin/bcftools [07:10:54] Found samtools - /usr/local/bin/samtools [07:10:54] Found java - /usr/local/bin/java [07:10:54] Found snpEff - /usr/local/bin/snpEff [07:10:54] Found samclip - /usr/local/bin/samclip [07:10:54] Found seqtk - /usr/local/bin/seqtk [07:10:54] Found parallel - /usr/local/bin/parallel [07:10:54] Found freebayes - /usr/local/bin/freebayes [07:10:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:10:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:10:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:10:54] Found vcfuniq - /usr/local/bin/vcfuniq [07:10:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:10:54] Found gzip - /bin/gzip [07:10:54] Found vt - /usr/local/bin/vt [07:10:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:10:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:10:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:10:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:10:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:10:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:10:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:10:55] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:11:21] This is snippy 4.6.0
Show full stderr[07:11:21] This is snippy 4.6.0 [07:11:21] Written by Torsten Seemann [07:11:21] Obtained from https://github.com/tseemann/snippy [07:11:21] Detected operating system: linux [07:11:21] Enabling bundled linux tools. [07:11:21] Found bwa - /usr/local/bin/bwa [07:11:21] Found bcftools - /usr/local/bin/bcftools [07:11:21] Found samtools - /usr/local/bin/samtools [07:11:21] Found java - /usr/local/bin/java [07:11:21] Found snpEff - /usr/local/bin/snpEff [07:11:21] Found samclip - /usr/local/bin/samclip [07:11:21] Found seqtk - /usr/local/bin/seqtk [07:11:21] Found parallel - /usr/local/bin/parallel [07:11:21] Found freebayes - /usr/local/bin/freebayes [07:11:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:11:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:11:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:11:21] Found vcfuniq - /usr/local/bin/vcfuniq [07:11:21] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:11:21] Found gzip - /bin/gzip [07:11:21] Found vt - /usr/local/bin/vt [07:11:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:11:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:11:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:11:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:11:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:11:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:11:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:11:22] Please supply a reference FASTA/GBK/EMBL file with --reference
1[08:28:34] This is snippy 4.6.0
Show full stderr[08:28:34] This is snippy 4.6.0 [08:28:34] Written by Torsten Seemann [08:28:34] Obtained from https://github.com/tseemann/snippy [08:28:34] Detected operating system: linux [08:28:34] Enabling bundled linux tools. [08:28:34] Found bwa - /usr/local/bin/bwa [08:28:34] Found bcftools - /usr/local/bin/bcftools [08:28:34] Found samtools - /usr/local/bin/samtools [08:28:34] Found java - /usr/local/bin/java [08:28:34] Found snpEff - /usr/local/bin/snpEff [08:28:34] Found samclip - /usr/local/bin/samclip [08:28:34] Found seqtk - /usr/local/bin/seqtk [08:28:34] Found parallel - /usr/local/bin/parallel [08:28:34] Found freebayes - /usr/local/bin/freebayes [08:28:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:28:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:28:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:28:34] Found vcfuniq - /usr/local/bin/vcfuniq [08:28:34] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:28:34] Found gzip - /bin/gzip [08:28:34] Found vt - /usr/local/bin/vt [08:28:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:28:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:28:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:28:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:28:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:28:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:28:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:28:35] Please supply a reference FASTA/GBK/EMBL file with --reference
1[08:33:31] This is snippy 4.6.0
Show full stderr[08:33:31] This is snippy 4.6.0 [08:33:31] Written by Torsten Seemann [08:33:31] Obtained from https://github.com/tseemann/snippy [08:33:31] Detected operating system: linux [08:33:31] Enabling bundled linux tools. [08:33:31] Found bwa - /usr/local/bin/bwa [08:33:31] Found bcftools - /usr/local/bin/bcftools [08:33:31] Found samtools - /usr/local/bin/samtools [08:33:31] Found java - /usr/local/bin/java [08:33:31] Found snpEff - /usr/local/bin/snpEff [08:33:31] Found samclip - /usr/local/bin/samclip [08:33:31] Found seqtk - /usr/local/bin/seqtk [08:33:31] Found parallel - /usr/local/bin/parallel [08:33:31] Found freebayes - /usr/local/bin/freebayes [08:33:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:33:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:33:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:33:31] Found vcfuniq - /usr/local/bin/vcfuniq [08:33:31] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:33:31] Found gzip - /bin/gzip [08:33:31] Found vt - /usr/local/bin/vt [08:33:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:33:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:33:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:33:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:33:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:33:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:33:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:33:32] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:12:35] This is snippy 4.6.0
Show full stderr[07:12:35] This is snippy 4.6.0 [07:12:35] Written by Torsten Seemann [07:12:35] Obtained from https://github.com/tseemann/snippy [07:12:35] Detected operating system: linux [07:12:35] Enabling bundled linux tools. [07:12:35] Found bwa - /usr/local/bin/bwa [07:12:35] Found bcftools - /usr/local/bin/bcftools [07:12:35] Found samtools - /usr/local/bin/samtools [07:12:35] Found java - /usr/local/bin/java [07:12:35] Found snpEff - /usr/local/bin/snpEff [07:12:35] Found samclip - /usr/local/bin/samclip [07:12:35] Found seqtk - /usr/local/bin/seqtk [07:12:35] Found parallel - /usr/local/bin/parallel [07:12:35] Found freebayes - /usr/local/bin/freebayes [07:12:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:12:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:12:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:12:35] Found vcfuniq - /usr/local/bin/vcfuniq [07:12:35] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:12:35] Found gzip - /bin/gzip [07:12:36] Found vt - /usr/local/bin/vt [07:12:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:12:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:12:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:12:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:12:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:12:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:12:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:12:36] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:13:14] This is snippy 4.6.0
Show full stderr[07:13:14] This is snippy 4.6.0 [07:13:14] Written by Torsten Seemann [07:13:14] Obtained from https://github.com/tseemann/snippy [07:13:14] Detected operating system: linux [07:13:14] Enabling bundled linux tools. [07:13:14] Found bwa - /usr/local/bin/bwa [07:13:14] Found bcftools - /usr/local/bin/bcftools [07:13:14] Found samtools - /usr/local/bin/samtools [07:13:14] Found java - /usr/local/bin/java [07:13:14] Found snpEff - /usr/local/bin/snpEff [07:13:14] Found samclip - /usr/local/bin/samclip [07:13:14] Found seqtk - /usr/local/bin/seqtk [07:13:14] Found parallel - /usr/local/bin/parallel [07:13:14] Found freebayes - /usr/local/bin/freebayes [07:13:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:13:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:13:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:13:14] Found vcfuniq - /usr/local/bin/vcfuniq [07:13:14] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:13:14] Found gzip - /bin/gzip [07:13:14] Found vt - /usr/local/bin/vt [07:13:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:13:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:13:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:13:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:13:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:13:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:13:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:13:15] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:13:02] This is snippy 4.6.0
Show full stderr[07:13:02] This is snippy 4.6.0 [07:13:02] Written by Torsten Seemann [07:13:02] Obtained from https://github.com/tseemann/snippy [07:13:02] Detected operating system: linux [07:13:02] Enabling bundled linux tools. [07:13:02] Found bwa - /usr/local/bin/bwa [07:13:02] Found bcftools - /usr/local/bin/bcftools [07:13:02] Found samtools - /usr/local/bin/samtools [07:13:02] Found java - /usr/local/bin/java [07:13:02] Found snpEff - /usr/local/bin/snpEff [07:13:02] Found samclip - /usr/local/bin/samclip [07:13:02] Found seqtk - /usr/local/bin/seqtk [07:13:02] Found parallel - /usr/local/bin/parallel [07:13:02] Found freebayes - /usr/local/bin/freebayes [07:13:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:13:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:13:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:13:02] Found vcfuniq - /usr/local/bin/vcfuniq [07:13:02] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:13:02] Found gzip - /bin/gzip [07:13:02] Found vt - /usr/local/bin/vt [07:13:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:13:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:13:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:13:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:13:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:13:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:13:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:13:02] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:13:01] This is snippy 4.6.0
Show full stderr[07:13:01] This is snippy 4.6.0 [07:13:01] Written by Torsten Seemann [07:13:01] Obtained from https://github.com/tseemann/snippy [07:13:01] Detected operating system: linux [07:13:01] Enabling bundled linux tools. [07:13:01] Found bwa - /usr/local/bin/bwa [07:13:01] Found bcftools - /usr/local/bin/bcftools [07:13:01] Found samtools - /usr/local/bin/samtools [07:13:01] Found java - /usr/local/bin/java [07:13:01] Found snpEff - /usr/local/bin/snpEff [07:13:01] Found samclip - /usr/local/bin/samclip [07:13:01] Found seqtk - /usr/local/bin/seqtk [07:13:01] Found parallel - /usr/local/bin/parallel [07:13:01] Found freebayes - /usr/local/bin/freebayes [07:13:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:13:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:13:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:13:02] Found vcfuniq - /usr/local/bin/vcfuniq [07:13:02] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:13:02] Found gzip - /bin/gzip [07:13:02] Found vt - /usr/local/bin/vt [07:13:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:13:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:13:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:13:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:13:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:13:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:13:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:13:02] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:15:55] This is snippy 4.6.0
Show full stderr[07:15:55] This is snippy 4.6.0 [07:15:55] Written by Torsten Seemann [07:15:55] Obtained from https://github.com/tseemann/snippy [07:15:55] Detected operating system: linux [07:15:55] Enabling bundled linux tools. [07:15:55] Found bwa - /usr/local/bin/bwa [07:15:55] Found bcftools - /usr/local/bin/bcftools [07:15:55] Found samtools - /usr/local/bin/samtools [07:15:55] Found java - /usr/local/bin/java [07:15:55] Found snpEff - /usr/local/bin/snpEff [07:15:55] Found samclip - /usr/local/bin/samclip [07:15:55] Found seqtk - /usr/local/bin/seqtk [07:15:55] Found parallel - /usr/local/bin/parallel [07:15:55] Found freebayes - /usr/local/bin/freebayes [07:15:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:15:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:15:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:15:55] Found vcfuniq - /usr/local/bin/vcfuniq [07:15:55] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:15:55] Found gzip - /bin/gzip [07:15:55] Found vt - /usr/local/bin/vt [07:15:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:15:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:15:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:15:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:15:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:15:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:15:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:15:56] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:14:57] This is snippy 4.6.0
Show full stderr[07:14:57] This is snippy 4.6.0 [07:14:57] Written by Torsten Seemann [07:14:57] Obtained from https://github.com/tseemann/snippy [07:14:57] Detected operating system: linux [07:14:57] Enabling bundled linux tools. [07:14:57] Found bwa - /usr/local/bin/bwa [07:14:57] Found bcftools - /usr/local/bin/bcftools [07:14:57] Found samtools - /usr/local/bin/samtools [07:14:57] Found java - /usr/local/bin/java [07:14:57] Found snpEff - /usr/local/bin/snpEff [07:14:57] Found samclip - /usr/local/bin/samclip [07:14:57] Found seqtk - /usr/local/bin/seqtk [07:14:57] Found parallel - /usr/local/bin/parallel [07:14:57] Found freebayes - /usr/local/bin/freebayes [07:14:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:14:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:14:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:14:57] Found vcfuniq - /usr/local/bin/vcfuniq [07:14:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:14:57] Found gzip - /bin/gzip [07:14:57] Found vt - /usr/local/bin/vt [07:14:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:14:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:14:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:14:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:14:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:14:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:14:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:14:58] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:15:27] This is snippy 4.6.0
Show full stderr[07:15:27] This is snippy 4.6.0 [07:15:27] Written by Torsten Seemann [07:15:27] Obtained from https://github.com/tseemann/snippy [07:15:27] Detected operating system: linux [07:15:27] Enabling bundled linux tools. [07:15:27] Found bwa - /usr/local/bin/bwa [07:15:27] Found bcftools - /usr/local/bin/bcftools [07:15:27] Found samtools - /usr/local/bin/samtools [07:15:27] Found java - /usr/local/bin/java [07:15:27] Found snpEff - /usr/local/bin/snpEff [07:15:27] Found samclip - /usr/local/bin/samclip [07:15:27] Found seqtk - /usr/local/bin/seqtk [07:15:27] Found parallel - /usr/local/bin/parallel [07:15:27] Found freebayes - /usr/local/bin/freebayes [07:15:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:15:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:15:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:15:27] Found vcfuniq - /usr/local/bin/vcfuniq [07:15:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:15:27] Found gzip - /bin/gzip [07:15:27] Found vt - /usr/local/bin/vt [07:15:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:15:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:15:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:15:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:15:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:15:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:15:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:15:28] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:15:38] This is snippy 4.6.0
Show full stderr[07:15:38] This is snippy 4.6.0 [07:15:38] Written by Torsten Seemann [07:15:38] Obtained from https://github.com/tseemann/snippy [07:15:38] Detected operating system: linux [07:15:38] Enabling bundled linux tools. [07:15:38] Found bwa - /usr/local/bin/bwa [07:15:38] Found bcftools - /usr/local/bin/bcftools [07:15:38] Found samtools - /usr/local/bin/samtools [07:15:38] Found java - /usr/local/bin/java [07:15:38] Found snpEff - /usr/local/bin/snpEff [07:15:38] Found samclip - /usr/local/bin/samclip [07:15:38] Found seqtk - /usr/local/bin/seqtk [07:15:38] Found parallel - /usr/local/bin/parallel [07:15:38] Found freebayes - /usr/local/bin/freebayes [07:15:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:15:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:15:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:15:38] Found vcfuniq - /usr/local/bin/vcfuniq [07:15:38] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:15:38] Found gzip - /bin/gzip [07:15:38] Found vt - /usr/local/bin/vt [07:15:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:15:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:15:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:15:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:15:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:15:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:15:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:15:39] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:15:52] This is snippy 4.6.0
Show full stderr[07:15:52] This is snippy 4.6.0 [07:15:52] Written by Torsten Seemann [07:15:52] Obtained from https://github.com/tseemann/snippy [07:15:52] Detected operating system: linux [07:15:52] Enabling bundled linux tools. [07:15:52] Found bwa - /usr/local/bin/bwa [07:15:52] Found bcftools - /usr/local/bin/bcftools [07:15:52] Found samtools - /usr/local/bin/samtools [07:15:52] Found java - /usr/local/bin/java [07:15:52] Found snpEff - /usr/local/bin/snpEff [07:15:52] Found samclip - /usr/local/bin/samclip [07:15:52] Found seqtk - /usr/local/bin/seqtk [07:15:52] Found parallel - /usr/local/bin/parallel [07:15:52] Found freebayes - /usr/local/bin/freebayes [07:15:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:15:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:15:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:15:52] Found vcfuniq - /usr/local/bin/vcfuniq [07:15:52] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:15:52] Found gzip - /bin/gzip [07:15:52] Found vt - /usr/local/bin/vt [07:15:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:15:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:15:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:15:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:15:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:15:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:15:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:15:53] Please supply a reference FASTA/GBK/EMBL file with --reference
1[08:45:37] This is snippy 4.6.0
Show full stderr[08:45:37] This is snippy 4.6.0 [08:45:37] Written by Torsten Seemann [08:45:37] Obtained from https://github.com/tseemann/snippy [08:45:37] Detected operating system: linux [08:45:37] Enabling bundled linux tools. [08:45:37] Found bwa - /usr/local/bin/bwa [08:45:37] Found bcftools - /usr/local/bin/bcftools [08:45:37] Found samtools - /usr/local/bin/samtools [08:45:37] Found java - /usr/local/bin/java [08:45:37] Found snpEff - /usr/local/bin/snpEff [08:45:37] Found samclip - /usr/local/bin/samclip [08:45:37] Found seqtk - /usr/local/bin/seqtk [08:45:37] Found parallel - /usr/local/bin/parallel [08:45:37] Found freebayes - /usr/local/bin/freebayes [08:45:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:45:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:45:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:45:37] Found vcfuniq - /usr/local/bin/vcfuniq [08:45:37] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:45:37] Found gzip - /bin/gzip [08:45:37] Found vt - /usr/local/bin/vt [08:45:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:45:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:45:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:45:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:45:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:45:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:45:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:45:38] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:16:10] This is snippy 4.6.0
Show full stderr[07:16:10] This is snippy 4.6.0 [07:16:10] Written by Torsten Seemann [07:16:10] Obtained from https://github.com/tseemann/snippy [07:16:10] Detected operating system: linux [07:16:10] Enabling bundled linux tools. [07:16:10] Found bwa - /usr/local/bin/bwa [07:16:10] Found bcftools - /usr/local/bin/bcftools [07:16:10] Found samtools - /usr/local/bin/samtools [07:16:10] Found java - /usr/local/bin/java [07:16:10] Found snpEff - /usr/local/bin/snpEff [07:16:10] Found samclip - /usr/local/bin/samclip [07:16:10] Found seqtk - /usr/local/bin/seqtk [07:16:10] Found parallel - /usr/local/bin/parallel [07:16:10] Found freebayes - /usr/local/bin/freebayes [07:16:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:16:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:16:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:16:10] Found vcfuniq - /usr/local/bin/vcfuniq [07:16:10] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:16:10] Found gzip - /bin/gzip [07:16:10] Found vt - /usr/local/bin/vt [07:16:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:16:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:16:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:16:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:16:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:16:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:16:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:16:11] Please supply a reference FASTA/GBK/EMBL file with --reference
1[08:03:33] This is snippy 4.6.0
Show full stderr[08:03:33] This is snippy 4.6.0 [08:03:33] Written by Torsten Seemann [08:03:33] Obtained from https://github.com/tseemann/snippy [08:03:33] Detected operating system: linux [08:03:33] Enabling bundled linux tools. [08:03:33] Found bwa - /usr/local/bin/bwa [08:03:33] Found bcftools - /usr/local/bin/bcftools [08:03:33] Found samtools - /usr/local/bin/samtools [08:03:33] Found java - /usr/local/bin/java [08:03:33] Found snpEff - /usr/local/bin/snpEff [08:03:33] Found samclip - /usr/local/bin/samclip [08:03:33] Found seqtk - /usr/local/bin/seqtk [08:03:33] Found parallel - /usr/local/bin/parallel [08:03:33] Found freebayes - /usr/local/bin/freebayes [08:03:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:03:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:03:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:03:33] Found vcfuniq - /usr/local/bin/vcfuniq [08:03:33] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:03:33] Found gzip - /bin/gzip [08:03:33] Found vt - /usr/local/bin/vt [08:03:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:03:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:03:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:03:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:03:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:03:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:03:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:03:34] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:15:13] This is snippy 4.6.0
Show full stderr[07:15:13] This is snippy 4.6.0 [07:15:13] Written by Torsten Seemann [07:15:13] Obtained from https://github.com/tseemann/snippy [07:15:13] Detected operating system: linux [07:15:13] Enabling bundled linux tools. [07:15:13] Found bwa - /usr/local/bin/bwa [07:15:13] Found bcftools - /usr/local/bin/bcftools [07:15:13] Found samtools - /usr/local/bin/samtools [07:15:13] Found java - /usr/local/bin/java [07:15:13] Found snpEff - /usr/local/bin/snpEff [07:15:13] Found samclip - /usr/local/bin/samclip [07:15:13] Found seqtk - /usr/local/bin/seqtk [07:15:13] Found parallel - /usr/local/bin/parallel [07:15:13] Found freebayes - /usr/local/bin/freebayes [07:15:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:15:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:15:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:15:13] Found vcfuniq - /usr/local/bin/vcfuniq [07:15:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:15:13] Found gzip - /bin/gzip [07:15:13] Found vt - /usr/local/bin/vt [07:15:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:15:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:15:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:15:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:15:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:15:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:15:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:15:14] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:15:24] This is snippy 4.6.0
Show full stderr[07:15:24] This is snippy 4.6.0 [07:15:24] Written by Torsten Seemann [07:15:24] Obtained from https://github.com/tseemann/snippy [07:15:24] Detected operating system: linux [07:15:24] Enabling bundled linux tools. [07:15:24] Found bwa - /usr/local/bin/bwa [07:15:24] Found bcftools - /usr/local/bin/bcftools [07:15:24] Found samtools - /usr/local/bin/samtools [07:15:24] Found java - /usr/local/bin/java [07:15:24] Found snpEff - /usr/local/bin/snpEff [07:15:24] Found samclip - /usr/local/bin/samclip [07:15:24] Found seqtk - /usr/local/bin/seqtk [07:15:24] Found parallel - /usr/local/bin/parallel [07:15:24] Found freebayes - /usr/local/bin/freebayes [07:15:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:15:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:15:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:15:24] Found vcfuniq - /usr/local/bin/vcfuniq [07:15:24] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:15:24] Found gzip - /bin/gzip [07:15:24] Found vt - /usr/local/bin/vt [07:15:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:15:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:15:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:15:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:15:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:15:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:15:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:15:25] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:16:07] This is snippy 4.6.0
Show full stderr[07:16:07] This is snippy 4.6.0 [07:16:07] Written by Torsten Seemann [07:16:07] Obtained from https://github.com/tseemann/snippy [07:16:07] Detected operating system: linux [07:16:07] Enabling bundled linux tools. [07:16:07] Found bwa - /usr/local/bin/bwa [07:16:07] Found bcftools - /usr/local/bin/bcftools [07:16:07] Found samtools - /usr/local/bin/samtools [07:16:07] Found java - /usr/local/bin/java [07:16:07] Found snpEff - /usr/local/bin/snpEff [07:16:07] Found samclip - /usr/local/bin/samclip [07:16:07] Found seqtk - /usr/local/bin/seqtk [07:16:07] Found parallel - /usr/local/bin/parallel [07:16:07] Found freebayes - /usr/local/bin/freebayes [07:16:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:16:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:16:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:16:07] Found vcfuniq - /usr/local/bin/vcfuniq [07:16:07] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:16:07] Found gzip - /bin/gzip [07:16:07] Found vt - /usr/local/bin/vt [07:16:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:16:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:16:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:16:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:16:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:16:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:16:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:16:08] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:16:19] This is snippy 4.6.0
Show full stderr[07:16:19] This is snippy 4.6.0 [07:16:19] Written by Torsten Seemann [07:16:19] Obtained from https://github.com/tseemann/snippy [07:16:19] Detected operating system: linux [07:16:19] Enabling bundled linux tools. [07:16:19] Found bwa - /usr/local/bin/bwa [07:16:19] Found bcftools - /usr/local/bin/bcftools [07:16:19] Found samtools - /usr/local/bin/samtools [07:16:19] Found java - /usr/local/bin/java [07:16:19] Found snpEff - /usr/local/bin/snpEff [07:16:19] Found samclip - /usr/local/bin/samclip [07:16:19] Found seqtk - /usr/local/bin/seqtk [07:16:19] Found parallel - /usr/local/bin/parallel [07:16:19] Found freebayes - /usr/local/bin/freebayes [07:16:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:16:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:16:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:16:19] Found vcfuniq - /usr/local/bin/vcfuniq [07:16:19] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:16:19] Found gzip - /bin/gzip [07:16:19] Found vt - /usr/local/bin/vt [07:16:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:16:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:16:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:16:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:16:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:16:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:16:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:16:20] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:29:19] This is snippy 4.6.0
Show full stderr[07:29:19] This is snippy 4.6.0 [07:29:19] Written by Torsten Seemann [07:29:19] Obtained from https://github.com/tseemann/snippy [07:29:19] Detected operating system: linux [07:29:19] Enabling bundled linux tools. [07:29:19] Found bwa - /usr/local/bin/bwa [07:29:19] Found bcftools - /usr/local/bin/bcftools [07:29:19] Found samtools - /usr/local/bin/samtools [07:29:19] Found java - /usr/local/bin/java [07:29:19] Found snpEff - /usr/local/bin/snpEff [07:29:19] Found samclip - /usr/local/bin/samclip [07:29:19] Found seqtk - /usr/local/bin/seqtk [07:29:19] Found parallel - /usr/local/bin/parallel [07:29:19] Found freebayes - /usr/local/bin/freebayes [07:29:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:29:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:29:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:29:19] Found vcfuniq - /usr/local/bin/vcfuniq [07:29:19] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:29:19] Found gzip - /bin/gzip [07:29:19] Found vt - /usr/local/bin/vt [07:29:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:29:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:29:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:29:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:29:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:29:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:29:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:29:20] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:31:57] This is snippy 4.6.0
Show full stderr[07:31:57] This is snippy 4.6.0 [07:31:57] Written by Torsten Seemann [07:31:57] Obtained from https://github.com/tseemann/snippy [07:31:57] Detected operating system: linux [07:31:57] Enabling bundled linux tools. [07:31:57] Found bwa - /usr/local/bin/bwa [07:31:57] Found bcftools - /usr/local/bin/bcftools [07:31:57] Found samtools - /usr/local/bin/samtools [07:31:57] Found java - /usr/local/bin/java [07:31:57] Found snpEff - /usr/local/bin/snpEff [07:31:57] Found samclip - /usr/local/bin/samclip [07:31:57] Found seqtk - /usr/local/bin/seqtk [07:31:57] Found parallel - /usr/local/bin/parallel [07:31:57] Found freebayes - /usr/local/bin/freebayes [07:31:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:31:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:31:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:31:57] Found vcfuniq - /usr/local/bin/vcfuniq [07:31:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:31:57] Found gzip - /bin/gzip [07:31:57] Found vt - /usr/local/bin/vt [07:31:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:31:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:31:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:31:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:31:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:31:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:31:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:31:58] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:29:04] This is snippy 4.6.0
Show full stderr[07:29:04] This is snippy 4.6.0 [07:29:04] Written by Torsten Seemann [07:29:04] Obtained from https://github.com/tseemann/snippy [07:29:04] Detected operating system: linux [07:29:04] Enabling bundled linux tools. [07:29:04] Found bwa - /usr/local/bin/bwa [07:29:04] Found bcftools - /usr/local/bin/bcftools [07:29:04] Found samtools - /usr/local/bin/samtools [07:29:04] Found java - /usr/local/bin/java [07:29:04] Found snpEff - /usr/local/bin/snpEff [07:29:04] Found samclip - /usr/local/bin/samclip [07:29:04] Found seqtk - /usr/local/bin/seqtk [07:29:04] Found parallel - /usr/local/bin/parallel [07:29:04] Found freebayes - /usr/local/bin/freebayes [07:29:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:29:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:29:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:29:04] Found vcfuniq - /usr/local/bin/vcfuniq [07:29:04] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:29:04] Found gzip - /bin/gzip [07:29:04] Found vt - /usr/local/bin/vt [07:29:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:29:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:29:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:29:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:29:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:29:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:29:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:29:05] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:29:49] This is snippy 4.6.0
Show full stderr[07:29:49] This is snippy 4.6.0 [07:29:49] Written by Torsten Seemann [07:29:49] Obtained from https://github.com/tseemann/snippy [07:29:49] Detected operating system: linux [07:29:49] Enabling bundled linux tools. [07:29:49] Found bwa - /usr/local/bin/bwa [07:29:49] Found bcftools - /usr/local/bin/bcftools [07:29:49] Found samtools - /usr/local/bin/samtools [07:29:49] Found java - /usr/local/bin/java [07:29:49] Found snpEff - /usr/local/bin/snpEff [07:29:49] Found samclip - /usr/local/bin/samclip [07:29:49] Found seqtk - /usr/local/bin/seqtk [07:29:49] Found parallel - /usr/local/bin/parallel [07:29:49] Found freebayes - /usr/local/bin/freebayes [07:29:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:29:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:29:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:29:49] Found vcfuniq - /usr/local/bin/vcfuniq [07:29:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:29:49] Found gzip - /bin/gzip [07:29:49] Found vt - /usr/local/bin/vt [07:29:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:29:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:29:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:29:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:29:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:29:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:29:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:29:50] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:28:12] This is snippy 4.6.0
Show full stderr[07:28:12] This is snippy 4.6.0 [07:28:12] Written by Torsten Seemann [07:28:12] Obtained from https://github.com/tseemann/snippy [07:28:12] Detected operating system: linux [07:28:12] Enabling bundled linux tools. [07:28:12] Found bwa - /usr/local/bin/bwa [07:28:12] Found bcftools - /usr/local/bin/bcftools [07:28:12] Found samtools - /usr/local/bin/samtools [07:28:12] Found java - /usr/local/bin/java [07:28:12] Found snpEff - /usr/local/bin/snpEff [07:28:12] Found samclip - /usr/local/bin/samclip [07:28:12] Found seqtk - /usr/local/bin/seqtk [07:28:12] Found parallel - /usr/local/bin/parallel [07:28:12] Found freebayes - /usr/local/bin/freebayes [07:28:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:28:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:28:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:28:13] Found vcfuniq - /usr/local/bin/vcfuniq [07:28:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:28:13] Found gzip - /bin/gzip [07:28:13] Found vt - /usr/local/bin/vt [07:28:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:28:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:28:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:28:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:28:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:28:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:28:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:28:13] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:28:15] This is snippy 4.6.0
Show full stderr[07:28:15] This is snippy 4.6.0 [07:28:15] Written by Torsten Seemann [07:28:15] Obtained from https://github.com/tseemann/snippy [07:28:15] Detected operating system: linux [07:28:15] Enabling bundled linux tools. [07:28:16] Found bwa - /usr/local/bin/bwa [07:28:16] Found bcftools - /usr/local/bin/bcftools [07:28:16] Found samtools - /usr/local/bin/samtools [07:28:16] Found java - /usr/local/bin/java [07:28:16] Found snpEff - /usr/local/bin/snpEff [07:28:16] Found samclip - /usr/local/bin/samclip [07:28:16] Found seqtk - /usr/local/bin/seqtk [07:28:16] Found parallel - /usr/local/bin/parallel [07:28:16] Found freebayes - /usr/local/bin/freebayes [07:28:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:28:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:28:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:28:16] Found vcfuniq - /usr/local/bin/vcfuniq [07:28:16] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:28:16] Found gzip - /bin/gzip [07:28:16] Found vt - /usr/local/bin/vt [07:28:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:28:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:28:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:28:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:28:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:28:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:28:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:28:16] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:28:25] This is snippy 4.6.0
Show full stderr[07:28:25] This is snippy 4.6.0 [07:28:25] Written by Torsten Seemann [07:28:25] Obtained from https://github.com/tseemann/snippy [07:28:25] Detected operating system: linux [07:28:25] Enabling bundled linux tools. [07:28:25] Found bwa - /usr/local/bin/bwa [07:28:25] Found bcftools - /usr/local/bin/bcftools [07:28:25] Found samtools - /usr/local/bin/samtools [07:28:25] Found java - /usr/local/bin/java [07:28:25] Found snpEff - /usr/local/bin/snpEff [07:28:26] Found samclip - /usr/local/bin/samclip [07:28:26] Found seqtk - /usr/local/bin/seqtk [07:28:26] Found parallel - /usr/local/bin/parallel [07:28:26] Found freebayes - /usr/local/bin/freebayes [07:28:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:28:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:28:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:28:26] Found vcfuniq - /usr/local/bin/vcfuniq [07:28:26] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:28:26] Found gzip - /bin/gzip [07:28:26] Found vt - /usr/local/bin/vt [07:28:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:28:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:28:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:28:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:28:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:28:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:28:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:28:26] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:28:28] This is snippy 4.6.0
Show full stderr[07:28:28] This is snippy 4.6.0 [07:28:28] Written by Torsten Seemann [07:28:28] Obtained from https://github.com/tseemann/snippy [07:28:28] Detected operating system: linux [07:28:28] Enabling bundled linux tools. [07:28:28] Found bwa - /usr/local/bin/bwa [07:28:28] Found bcftools - /usr/local/bin/bcftools [07:28:28] Found samtools - /usr/local/bin/samtools [07:28:28] Found java - /usr/local/bin/java [07:28:29] Found snpEff - /usr/local/bin/snpEff [07:28:29] Found samclip - /usr/local/bin/samclip [07:28:29] Found seqtk - /usr/local/bin/seqtk [07:28:29] Found parallel - /usr/local/bin/parallel [07:28:29] Found freebayes - /usr/local/bin/freebayes [07:28:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:28:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:28:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:28:29] Found vcfuniq - /usr/local/bin/vcfuniq [07:28:29] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:28:29] Found gzip - /bin/gzip [07:28:29] Found vt - /usr/local/bin/vt [07:28:29] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:28:29] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:28:29] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:28:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:28:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:28:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:28:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:28:29] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:29:22] This is snippy 4.6.0
Show full stderr[07:29:22] This is snippy 4.6.0 [07:29:22] Written by Torsten Seemann [07:29:22] Obtained from https://github.com/tseemann/snippy [07:29:22] Detected operating system: linux [07:29:22] Enabling bundled linux tools. [07:29:22] Found bwa - /usr/local/bin/bwa [07:29:22] Found bcftools - /usr/local/bin/bcftools [07:29:22] Found samtools - /usr/local/bin/samtools [07:29:22] Found java - /usr/local/bin/java [07:29:22] Found snpEff - /usr/local/bin/snpEff [07:29:22] Found samclip - /usr/local/bin/samclip [07:29:22] Found seqtk - /usr/local/bin/seqtk [07:29:22] Found parallel - /usr/local/bin/parallel [07:29:22] Found freebayes - /usr/local/bin/freebayes [07:29:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:29:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:29:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:29:22] Found vcfuniq - /usr/local/bin/vcfuniq [07:29:22] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:29:22] Found gzip - /bin/gzip [07:29:22] Found vt - /usr/local/bin/vt [07:29:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:29:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:29:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:29:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:29:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:29:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:29:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:29:22] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:29:40] This is snippy 4.6.0
Show full stderr[07:29:40] This is snippy 4.6.0 [07:29:40] Written by Torsten Seemann [07:29:40] Obtained from https://github.com/tseemann/snippy [07:29:40] Detected operating system: linux [07:29:40] Enabling bundled linux tools. [07:29:40] Found bwa - /usr/local/bin/bwa [07:29:40] Found bcftools - /usr/local/bin/bcftools [07:29:40] Found samtools - /usr/local/bin/samtools [07:29:40] Found java - /usr/local/bin/java [07:29:40] Found snpEff - /usr/local/bin/snpEff [07:29:40] Found samclip - /usr/local/bin/samclip [07:29:40] Found seqtk - /usr/local/bin/seqtk [07:29:40] Found parallel - /usr/local/bin/parallel [07:29:40] Found freebayes - /usr/local/bin/freebayes [07:29:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:29:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:29:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:29:40] Found vcfuniq - /usr/local/bin/vcfuniq [07:29:40] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:29:40] Found gzip - /bin/gzip [07:29:40] Found vt - /usr/local/bin/vt [07:29:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:29:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:29:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:29:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:29:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:29:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:29:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:29:41] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:29:07] This is snippy 4.6.0
Show full stderr[07:29:07] This is snippy 4.6.0 [07:29:07] Written by Torsten Seemann [07:29:07] Obtained from https://github.com/tseemann/snippy [07:29:07] Detected operating system: linux [07:29:07] Enabling bundled linux tools. [07:29:07] Found bwa - /usr/local/bin/bwa [07:29:07] Found bcftools - /usr/local/bin/bcftools [07:29:07] Found samtools - /usr/local/bin/samtools [07:29:07] Found java - /usr/local/bin/java [07:29:07] Found snpEff - /usr/local/bin/snpEff [07:29:07] Found samclip - /usr/local/bin/samclip [07:29:07] Found seqtk - /usr/local/bin/seqtk [07:29:07] Found parallel - /usr/local/bin/parallel [07:29:07] Found freebayes - /usr/local/bin/freebayes [07:29:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:29:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:29:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:29:07] Found vcfuniq - /usr/local/bin/vcfuniq [07:29:07] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:29:07] Found gzip - /bin/gzip [07:29:07] Found vt - /usr/local/bin/vt [07:29:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:29:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:29:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:29:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:29:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:29:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:29:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:29:08] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:30:22] This is snippy 4.6.0
Show full stderr[07:30:22] This is snippy 4.6.0 [07:30:22] Written by Torsten Seemann [07:30:22] Obtained from https://github.com/tseemann/snippy [07:30:22] Detected operating system: linux [07:30:22] Enabling bundled linux tools. [07:30:22] Found bwa - /usr/local/bin/bwa [07:30:22] Found bcftools - /usr/local/bin/bcftools [07:30:22] Found samtools - /usr/local/bin/samtools [07:30:22] Found java - /usr/local/bin/java [07:30:22] Found snpEff - /usr/local/bin/snpEff [07:30:22] Found samclip - /usr/local/bin/samclip [07:30:22] Found seqtk - /usr/local/bin/seqtk [07:30:22] Found parallel - /usr/local/bin/parallel [07:30:22] Found freebayes - /usr/local/bin/freebayes [07:30:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:30:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:30:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:30:22] Found vcfuniq - /usr/local/bin/vcfuniq [07:30:22] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:30:22] Found gzip - /bin/gzip [07:30:22] Found vt - /usr/local/bin/vt [07:30:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:30:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:30:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:30:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:30:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:30:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:30:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:30:23] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:30:54] This is snippy 4.6.0
Show full stderr[07:30:54] This is snippy 4.6.0 [07:30:54] Written by Torsten Seemann [07:30:54] Obtained from https://github.com/tseemann/snippy [07:30:54] Detected operating system: linux [07:30:54] Enabling bundled linux tools. [07:30:54] Found bwa - /usr/local/bin/bwa [07:30:54] Found bcftools - /usr/local/bin/bcftools [07:30:54] Found samtools - /usr/local/bin/samtools [07:30:54] Found java - /usr/local/bin/java [07:30:54] Found snpEff - /usr/local/bin/snpEff [07:30:54] Found samclip - /usr/local/bin/samclip [07:30:54] Found seqtk - /usr/local/bin/seqtk [07:30:54] Found parallel - /usr/local/bin/parallel [07:30:54] Found freebayes - /usr/local/bin/freebayes [07:30:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:30:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:30:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:30:54] Found vcfuniq - /usr/local/bin/vcfuniq [07:30:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:30:54] Found gzip - /bin/gzip [07:30:54] Found vt - /usr/local/bin/vt [07:30:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:30:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:30:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:30:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:30:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:30:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:30:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:30:55] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:31:28] This is snippy 4.6.0
Show full stderr[07:31:28] This is snippy 4.6.0 [07:31:28] Written by Torsten Seemann [07:31:28] Obtained from https://github.com/tseemann/snippy [07:31:28] Detected operating system: linux [07:31:28] Enabling bundled linux tools. [07:31:28] Found bwa - /usr/local/bin/bwa [07:31:28] Found bcftools - /usr/local/bin/bcftools [07:31:28] Found samtools - /usr/local/bin/samtools [07:31:28] Found java - /usr/local/bin/java [07:31:28] Found snpEff - /usr/local/bin/snpEff [07:31:28] Found samclip - /usr/local/bin/samclip [07:31:28] Found seqtk - /usr/local/bin/seqtk [07:31:28] Found parallel - /usr/local/bin/parallel [07:31:28] Found freebayes - /usr/local/bin/freebayes [07:31:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:31:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:31:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:31:28] Found vcfuniq - /usr/local/bin/vcfuniq [07:31:28] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:31:28] Found gzip - /bin/gzip [07:31:28] Found vt - /usr/local/bin/vt [07:31:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:31:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:31:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:31:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:31:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:31:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:31:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:31:29] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:32:24] This is snippy 4.6.0
Show full stderr[07:32:24] This is snippy 4.6.0 [07:32:24] Written by Torsten Seemann [07:32:24] Obtained from https://github.com/tseemann/snippy [07:32:24] Detected operating system: linux [07:32:24] Enabling bundled linux tools. [07:32:24] Found bwa - /usr/local/bin/bwa [07:32:24] Found bcftools - /usr/local/bin/bcftools [07:32:24] Found samtools - /usr/local/bin/samtools [07:32:24] Found java - /usr/local/bin/java [07:32:24] Found snpEff - /usr/local/bin/snpEff [07:32:24] Found samclip - /usr/local/bin/samclip [07:32:24] Found seqtk - /usr/local/bin/seqtk [07:32:24] Found parallel - /usr/local/bin/parallel [07:32:24] Found freebayes - /usr/local/bin/freebayes [07:32:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:32:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:32:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:32:24] Found vcfuniq - /usr/local/bin/vcfuniq [07:32:24] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:32:24] Found gzip - /bin/gzip [07:32:24] Found vt - /usr/local/bin/vt [07:32:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:32:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:32:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:32:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:32:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:32:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:32:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:32:25] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:35:48] This is snippy 4.6.0
Show full stderr[07:35:48] This is snippy 4.6.0 [07:35:48] Written by Torsten Seemann [07:35:48] Obtained from https://github.com/tseemann/snippy [07:35:48] Detected operating system: linux [07:35:48] Enabling bundled linux tools. [07:35:48] Found bwa - /usr/local/bin/bwa [07:35:48] Found bcftools - /usr/local/bin/bcftools [07:35:48] Found samtools - /usr/local/bin/samtools [07:35:48] Found java - /usr/local/bin/java [07:35:48] Found snpEff - /usr/local/bin/snpEff [07:35:48] Found samclip - /usr/local/bin/samclip [07:35:48] Found seqtk - /usr/local/bin/seqtk [07:35:48] Found parallel - /usr/local/bin/parallel [07:35:48] Found freebayes - /usr/local/bin/freebayes [07:35:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:35:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:35:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:35:48] Found vcfuniq - /usr/local/bin/vcfuniq [07:35:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:35:48] Found gzip - /bin/gzip [07:35:48] Found vt - /usr/local/bin/vt [07:35:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:35:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:35:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:35:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:35:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:35:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:35:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:35:49] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:35:51] This is snippy 4.6.0
Show full stderr[07:35:51] This is snippy 4.6.0 [07:35:51] Written by Torsten Seemann [07:35:51] Obtained from https://github.com/tseemann/snippy [07:35:51] Detected operating system: linux [07:35:51] Enabling bundled linux tools. [07:35:51] Found bwa - /usr/local/bin/bwa [07:35:51] Found bcftools - /usr/local/bin/bcftools [07:35:51] Found samtools - /usr/local/bin/samtools [07:35:51] Found java - /usr/local/bin/java [07:35:51] Found snpEff - /usr/local/bin/snpEff [07:35:51] Found samclip - /usr/local/bin/samclip [07:35:51] Found seqtk - /usr/local/bin/seqtk [07:35:51] Found parallel - /usr/local/bin/parallel [07:35:51] Found freebayes - /usr/local/bin/freebayes [07:35:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:35:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:35:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:35:51] Found vcfuniq - /usr/local/bin/vcfuniq [07:35:51] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:35:51] Found gzip - /bin/gzip [07:35:51] Found vt - /usr/local/bin/vt [07:35:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:35:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:35:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:35:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:35:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:35:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:35:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:35:52] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:35:54] This is snippy 4.6.0
Show full stderr[07:35:54] This is snippy 4.6.0 [07:35:54] Written by Torsten Seemann [07:35:54] Obtained from https://github.com/tseemann/snippy [07:35:54] Detected operating system: linux [07:35:54] Enabling bundled linux tools. [07:35:54] Found bwa - /usr/local/bin/bwa [07:35:54] Found bcftools - /usr/local/bin/bcftools [07:35:54] Found samtools - /usr/local/bin/samtools [07:35:54] Found java - /usr/local/bin/java [07:35:54] Found snpEff - /usr/local/bin/snpEff [07:35:54] Found samclip - /usr/local/bin/samclip [07:35:54] Found seqtk - /usr/local/bin/seqtk [07:35:54] Found parallel - /usr/local/bin/parallel [07:35:54] Found freebayes - /usr/local/bin/freebayes [07:35:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:35:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:35:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:35:54] Found vcfuniq - /usr/local/bin/vcfuniq [07:35:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:35:54] Found gzip - /bin/gzip [07:35:54] Found vt - /usr/local/bin/vt [07:35:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:35:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:35:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:35:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:35:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:35:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:35:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:35:55] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:36:04] This is snippy 4.6.0
Show full stderr[07:36:04] This is snippy 4.6.0 [07:36:04] Written by Torsten Seemann [07:36:04] Obtained from https://github.com/tseemann/snippy [07:36:04] Detected operating system: linux [07:36:04] Enabling bundled linux tools. [07:36:04] Found bwa - /usr/local/bin/bwa [07:36:04] Found bcftools - /usr/local/bin/bcftools [07:36:04] Found samtools - /usr/local/bin/samtools [07:36:04] Found java - /usr/local/bin/java [07:36:04] Found snpEff - /usr/local/bin/snpEff [07:36:04] Found samclip - /usr/local/bin/samclip [07:36:04] Found seqtk - /usr/local/bin/seqtk [07:36:04] Found parallel - /usr/local/bin/parallel [07:36:04] Found freebayes - /usr/local/bin/freebayes [07:36:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:36:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:36:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:36:04] Found vcfuniq - /usr/local/bin/vcfuniq [07:36:04] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:36:04] Found gzip - /bin/gzip [07:36:04] Found vt - /usr/local/bin/vt [07:36:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:36:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:36:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:36:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:36:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:36:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:36:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:36:05] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:29:55] This is snippy 4.6.0
Show full stderr[07:29:55] This is snippy 4.6.0 [07:29:55] Written by Torsten Seemann [07:29:55] Obtained from https://github.com/tseemann/snippy [07:29:55] Detected operating system: linux [07:29:55] Enabling bundled linux tools. [07:29:55] Found bwa - /usr/local/bin/bwa [07:29:55] Found bcftools - /usr/local/bin/bcftools [07:29:55] Found samtools - /usr/local/bin/samtools [07:29:55] Found java - /usr/local/bin/java [07:29:55] Found snpEff - /usr/local/bin/snpEff [07:29:55] Found samclip - /usr/local/bin/samclip [07:29:55] Found seqtk - /usr/local/bin/seqtk [07:29:55] Found parallel - /usr/local/bin/parallel [07:29:55] Found freebayes - /usr/local/bin/freebayes [07:29:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:29:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:29:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:29:55] Found vcfuniq - /usr/local/bin/vcfuniq [07:29:55] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:29:55] Found gzip - /bin/gzip [07:29:55] Found vt - /usr/local/bin/vt [07:29:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:29:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:29:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:29:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:29:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:29:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:29:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:29:56] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:30:07] This is snippy 4.6.0
Show full stderr[07:30:07] This is snippy 4.6.0 [07:30:07] Written by Torsten Seemann [07:30:07] Obtained from https://github.com/tseemann/snippy [07:30:07] Detected operating system: linux [07:30:07] Enabling bundled linux tools. [07:30:07] Found bwa - /usr/local/bin/bwa [07:30:07] Found bcftools - /usr/local/bin/bcftools [07:30:07] Found samtools - /usr/local/bin/samtools [07:30:07] Found java - /usr/local/bin/java [07:30:07] Found snpEff - /usr/local/bin/snpEff [07:30:07] Found samclip - /usr/local/bin/samclip [07:30:07] Found seqtk - /usr/local/bin/seqtk [07:30:07] Found parallel - /usr/local/bin/parallel [07:30:07] Found freebayes - /usr/local/bin/freebayes [07:30:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:30:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:30:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:30:07] Found vcfuniq - /usr/local/bin/vcfuniq [07:30:07] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:30:07] Found gzip - /bin/gzip [07:30:07] Found vt - /usr/local/bin/vt [07:30:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:30:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:30:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:30:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:30:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:30:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:30:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:30:08] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:30:13] This is snippy 4.6.0
Show full stderr[07:30:13] This is snippy 4.6.0 [07:30:13] Written by Torsten Seemann [07:30:13] Obtained from https://github.com/tseemann/snippy [07:30:13] Detected operating system: linux [07:30:13] Enabling bundled linux tools. [07:30:13] Found bwa - /usr/local/bin/bwa [07:30:13] Found bcftools - /usr/local/bin/bcftools [07:30:13] Found samtools - /usr/local/bin/samtools [07:30:13] Found java - /usr/local/bin/java [07:30:13] Found snpEff - /usr/local/bin/snpEff [07:30:13] Found samclip - /usr/local/bin/samclip [07:30:13] Found seqtk - /usr/local/bin/seqtk [07:30:13] Found parallel - /usr/local/bin/parallel [07:30:13] Found freebayes - /usr/local/bin/freebayes [07:30:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:30:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:30:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:30:13] Found vcfuniq - /usr/local/bin/vcfuniq [07:30:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:30:13] Found gzip - /bin/gzip [07:30:13] Found vt - /usr/local/bin/vt [07:30:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:30:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:30:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:30:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:30:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:30:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:30:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:30:14] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:30:43] This is snippy 4.6.0
Show full stderr[07:30:43] This is snippy 4.6.0 [07:30:43] Written by Torsten Seemann [07:30:43] Obtained from https://github.com/tseemann/snippy [07:30:43] Detected operating system: linux [07:30:43] Enabling bundled linux tools. [07:30:43] Found bwa - /usr/local/bin/bwa [07:30:43] Found bcftools - /usr/local/bin/bcftools [07:30:43] Found samtools - /usr/local/bin/samtools [07:30:43] Found java - /usr/local/bin/java [07:30:43] Found snpEff - /usr/local/bin/snpEff [07:30:43] Found samclip - /usr/local/bin/samclip [07:30:43] Found seqtk - /usr/local/bin/seqtk [07:30:43] Found parallel - /usr/local/bin/parallel [07:30:43] Found freebayes - /usr/local/bin/freebayes [07:30:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:30:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:30:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:30:43] Found vcfuniq - /usr/local/bin/vcfuniq [07:30:43] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:30:43] Found gzip - /bin/gzip [07:30:43] Found vt - /usr/local/bin/vt [07:30:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:30:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:30:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:30:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:30:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:30:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:30:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:30:44] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:30:46] This is snippy 4.6.0
Show full stderr[07:30:46] This is snippy 4.6.0 [07:30:46] Written by Torsten Seemann [07:30:46] Obtained from https://github.com/tseemann/snippy [07:30:46] Detected operating system: linux [07:30:46] Enabling bundled linux tools. [07:30:46] Found bwa - /usr/local/bin/bwa [07:30:46] Found bcftools - /usr/local/bin/bcftools [07:30:46] Found samtools - /usr/local/bin/samtools [07:30:46] Found java - /usr/local/bin/java [07:30:46] Found snpEff - /usr/local/bin/snpEff [07:30:46] Found samclip - /usr/local/bin/samclip [07:30:46] Found seqtk - /usr/local/bin/seqtk [07:30:46] Found parallel - /usr/local/bin/parallel [07:30:46] Found freebayes - /usr/local/bin/freebayes [07:30:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:30:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:30:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:30:46] Found vcfuniq - /usr/local/bin/vcfuniq [07:30:46] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:30:46] Found gzip - /bin/gzip [07:30:46] Found vt - /usr/local/bin/vt [07:30:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:30:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:30:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:30:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:30:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:30:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:30:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:30:47] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:31:00] This is snippy 4.6.0
Show full stderr[07:31:00] This is snippy 4.6.0 [07:31:00] Written by Torsten Seemann [07:31:00] Obtained from https://github.com/tseemann/snippy [07:31:00] Detected operating system: linux [07:31:00] Enabling bundled linux tools. [07:31:00] Found bwa - /usr/local/bin/bwa [07:31:00] Found bcftools - /usr/local/bin/bcftools [07:31:00] Found samtools - /usr/local/bin/samtools [07:31:00] Found java - /usr/local/bin/java [07:31:00] Found snpEff - /usr/local/bin/snpEff [07:31:00] Found samclip - /usr/local/bin/samclip [07:31:00] Found seqtk - /usr/local/bin/seqtk [07:31:00] Found parallel - /usr/local/bin/parallel [07:31:00] Found freebayes - /usr/local/bin/freebayes [07:31:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:31:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:31:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:31:00] Found vcfuniq - /usr/local/bin/vcfuniq [07:31:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:31:00] Found gzip - /bin/gzip [07:31:00] Found vt - /usr/local/bin/vt [07:31:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:31:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:31:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:31:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:31:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:31:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:31:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:31:01] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:33:47] This is snippy 4.6.0
Show full stderr[07:33:47] This is snippy 4.6.0 [07:33:47] Written by Torsten Seemann [07:33:47] Obtained from https://github.com/tseemann/snippy [07:33:47] Detected operating system: linux [07:33:47] Enabling bundled linux tools. [07:33:47] Found bwa - /usr/local/bin/bwa [07:33:47] Found bcftools - /usr/local/bin/bcftools [07:33:47] Found samtools - /usr/local/bin/samtools [07:33:47] Found java - /usr/local/bin/java [07:33:47] Found snpEff - /usr/local/bin/snpEff [07:33:47] Found samclip - /usr/local/bin/samclip [07:33:47] Found seqtk - /usr/local/bin/seqtk [07:33:47] Found parallel - /usr/local/bin/parallel [07:33:47] Found freebayes - /usr/local/bin/freebayes [07:33:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:33:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:33:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:33:47] Found vcfuniq - /usr/local/bin/vcfuniq [07:33:47] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:33:47] Found gzip - /bin/gzip [07:33:47] Found vt - /usr/local/bin/vt [07:33:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:33:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:33:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:33:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:33:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:33:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:33:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:33:48] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:34:40] This is snippy 4.6.0
Show full stderr[07:34:40] This is snippy 4.6.0 [07:34:40] Written by Torsten Seemann [07:34:40] Obtained from https://github.com/tseemann/snippy [07:34:40] Detected operating system: linux [07:34:40] Enabling bundled linux tools. [07:34:40] Found bwa - /usr/local/bin/bwa [07:34:40] Found bcftools - /usr/local/bin/bcftools [07:34:40] Found samtools - /usr/local/bin/samtools [07:34:40] Found java - /usr/local/bin/java [07:34:40] Found snpEff - /usr/local/bin/snpEff [07:34:40] Found samclip - /usr/local/bin/samclip [07:34:40] Found seqtk - /usr/local/bin/seqtk [07:34:40] Found parallel - /usr/local/bin/parallel [07:34:40] Found freebayes - /usr/local/bin/freebayes [07:34:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:34:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:34:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:34:40] Found vcfuniq - /usr/local/bin/vcfuniq [07:34:40] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:34:40] Found gzip - /bin/gzip [07:34:40] Found vt - /usr/local/bin/vt [07:34:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:34:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:34:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:34:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:34:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:34:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:34:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:34:41] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:34:43] This is snippy 4.6.0
Show full stderr[07:34:43] This is snippy 4.6.0 [07:34:43] Written by Torsten Seemann [07:34:43] Obtained from https://github.com/tseemann/snippy [07:34:43] Detected operating system: linux [07:34:43] Enabling bundled linux tools. [07:34:43] Found bwa - /usr/local/bin/bwa [07:34:43] Found bcftools - /usr/local/bin/bcftools [07:34:43] Found samtools - /usr/local/bin/samtools [07:34:43] Found java - /usr/local/bin/java [07:34:43] Found snpEff - /usr/local/bin/snpEff [07:34:43] Found samclip - /usr/local/bin/samclip [07:34:43] Found seqtk - /usr/local/bin/seqtk [07:34:43] Found parallel - /usr/local/bin/parallel [07:34:43] Found freebayes - /usr/local/bin/freebayes [07:34:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:34:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:34:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:34:43] Found vcfuniq - /usr/local/bin/vcfuniq [07:34:43] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:34:43] Found gzip - /bin/gzip [07:34:43] Found vt - /usr/local/bin/vt [07:34:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:34:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:34:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:34:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:34:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:34:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:34:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:34:44] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:35:07] This is snippy 4.6.0
Show full stderr[07:35:07] This is snippy 4.6.0 [07:35:07] Written by Torsten Seemann [07:35:07] Obtained from https://github.com/tseemann/snippy [07:35:07] Detected operating system: linux [07:35:07] Enabling bundled linux tools. [07:35:07] Found bwa - /usr/local/bin/bwa [07:35:07] Found bcftools - /usr/local/bin/bcftools [07:35:07] Found samtools - /usr/local/bin/samtools [07:35:07] Found java - /usr/local/bin/java [07:35:07] Found snpEff - /usr/local/bin/snpEff [07:35:07] Found samclip - /usr/local/bin/samclip [07:35:07] Found seqtk - /usr/local/bin/seqtk [07:35:07] Found parallel - /usr/local/bin/parallel [07:35:07] Found freebayes - /usr/local/bin/freebayes [07:35:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:35:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:35:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:35:07] Found vcfuniq - /usr/local/bin/vcfuniq [07:35:07] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:35:07] Found gzip - /bin/gzip [07:35:07] Found vt - /usr/local/bin/vt [07:35:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:35:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:35:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:35:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:35:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:35:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:35:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:35:08] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:35:24] This is snippy 4.6.0
Show full stderr[07:35:24] This is snippy 4.6.0 [07:35:24] Written by Torsten Seemann [07:35:24] Obtained from https://github.com/tseemann/snippy [07:35:24] Detected operating system: linux [07:35:24] Enabling bundled linux tools. [07:35:24] Found bwa - /usr/local/bin/bwa [07:35:24] Found bcftools - /usr/local/bin/bcftools [07:35:24] Found samtools - /usr/local/bin/samtools [07:35:24] Found java - /usr/local/bin/java [07:35:24] Found snpEff - /usr/local/bin/snpEff [07:35:24] Found samclip - /usr/local/bin/samclip [07:35:24] Found seqtk - /usr/local/bin/seqtk [07:35:24] Found parallel - /usr/local/bin/parallel [07:35:24] Found freebayes - /usr/local/bin/freebayes [07:35:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:35:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:35:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:35:24] Found vcfuniq - /usr/local/bin/vcfuniq [07:35:24] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:35:24] Found gzip - /bin/gzip [07:35:24] Found vt - /usr/local/bin/vt [07:35:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:35:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:35:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:35:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:35:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:35:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:35:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:35:25] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:32:42] This is snippy 4.6.0
Show full stderr[07:32:42] This is snippy 4.6.0 [07:32:42] Written by Torsten Seemann [07:32:42] Obtained from https://github.com/tseemann/snippy [07:32:42] Detected operating system: linux [07:32:42] Enabling bundled linux tools. [07:32:42] Found bwa - /usr/local/bin/bwa [07:32:42] Found bcftools - /usr/local/bin/bcftools [07:32:42] Found samtools - /usr/local/bin/samtools [07:32:42] Found java - /usr/local/bin/java [07:32:42] Found snpEff - /usr/local/bin/snpEff [07:32:42] Found samclip - /usr/local/bin/samclip [07:32:42] Found seqtk - /usr/local/bin/seqtk [07:32:42] Found parallel - /usr/local/bin/parallel [07:32:42] Found freebayes - /usr/local/bin/freebayes [07:32:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:32:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:32:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:32:42] Found vcfuniq - /usr/local/bin/vcfuniq [07:32:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:32:42] Found gzip - /bin/gzip [07:32:42] Found vt - /usr/local/bin/vt [07:32:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:32:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:32:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:32:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:32:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:32:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:32:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:32:43] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:33:29] This is snippy 4.6.0
Show full stderr[07:33:29] This is snippy 4.6.0 [07:33:29] Written by Torsten Seemann [07:33:29] Obtained from https://github.com/tseemann/snippy [07:33:29] Detected operating system: linux [07:33:29] Enabling bundled linux tools. [07:33:29] Found bwa - /usr/local/bin/bwa [07:33:29] Found bcftools - /usr/local/bin/bcftools [07:33:29] Found samtools - /usr/local/bin/samtools [07:33:29] Found java - /usr/local/bin/java [07:33:29] Found snpEff - /usr/local/bin/snpEff [07:33:29] Found samclip - /usr/local/bin/samclip [07:33:29] Found seqtk - /usr/local/bin/seqtk [07:33:29] Found parallel - /usr/local/bin/parallel [07:33:29] Found freebayes - /usr/local/bin/freebayes [07:33:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:33:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:33:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:33:29] Found vcfuniq - /usr/local/bin/vcfuniq [07:33:29] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:33:29] Found gzip - /bin/gzip [07:33:29] Found vt - /usr/local/bin/vt [07:33:29] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:33:29] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:33:29] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:33:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:33:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:33:30] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:33:30] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:33:30] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:34:10] This is snippy 4.6.0
Show full stderr[07:34:10] This is snippy 4.6.0 [07:34:10] Written by Torsten Seemann [07:34:10] Obtained from https://github.com/tseemann/snippy [07:34:10] Detected operating system: linux [07:34:10] Enabling bundled linux tools. [07:34:10] Found bwa - /usr/local/bin/bwa [07:34:10] Found bcftools - /usr/local/bin/bcftools [07:34:10] Found samtools - /usr/local/bin/samtools [07:34:10] Found java - /usr/local/bin/java [07:34:10] Found snpEff - /usr/local/bin/snpEff [07:34:10] Found samclip - /usr/local/bin/samclip [07:34:10] Found seqtk - /usr/local/bin/seqtk [07:34:10] Found parallel - /usr/local/bin/parallel [07:34:10] Found freebayes - /usr/local/bin/freebayes [07:34:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:34:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:34:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:34:10] Found vcfuniq - /usr/local/bin/vcfuniq [07:34:10] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:34:10] Found gzip - /bin/gzip [07:34:10] Found vt - /usr/local/bin/vt [07:34:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:34:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:34:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:34:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:34:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:34:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:34:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:34:11] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:34:13] This is snippy 4.6.0
Show full stderr[07:34:13] This is snippy 4.6.0 [07:34:13] Written by Torsten Seemann [07:34:13] Obtained from https://github.com/tseemann/snippy [07:34:13] Detected operating system: linux [07:34:13] Enabling bundled linux tools. [07:34:13] Found bwa - /usr/local/bin/bwa [07:34:13] Found bcftools - /usr/local/bin/bcftools [07:34:13] Found samtools - /usr/local/bin/samtools [07:34:13] Found java - /usr/local/bin/java [07:34:13] Found snpEff - /usr/local/bin/snpEff [07:34:13] Found samclip - /usr/local/bin/samclip [07:34:13] Found seqtk - /usr/local/bin/seqtk [07:34:13] Found parallel - /usr/local/bin/parallel [07:34:13] Found freebayes - /usr/local/bin/freebayes [07:34:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:34:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:34:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:34:13] Found vcfuniq - /usr/local/bin/vcfuniq [07:34:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:34:13] Found gzip - /bin/gzip [07:34:13] Found vt - /usr/local/bin/vt [07:34:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:34:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:34:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:34:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:34:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:34:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:34:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:34:14] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:34:58] This is snippy 4.6.0
Show full stderr[07:34:58] This is snippy 4.6.0 [07:34:58] Written by Torsten Seemann [07:34:58] Obtained from https://github.com/tseemann/snippy [07:34:58] Detected operating system: linux [07:34:58] Enabling bundled linux tools. [07:34:58] Found bwa - /usr/local/bin/bwa [07:34:58] Found bcftools - /usr/local/bin/bcftools [07:34:58] Found samtools - /usr/local/bin/samtools [07:34:58] Found java - /usr/local/bin/java [07:34:58] Found snpEff - /usr/local/bin/snpEff [07:34:58] Found samclip - /usr/local/bin/samclip [07:34:58] Found seqtk - /usr/local/bin/seqtk [07:34:58] Found parallel - /usr/local/bin/parallel [07:34:58] Found freebayes - /usr/local/bin/freebayes [07:34:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:34:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:34:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:34:58] Found vcfuniq - /usr/local/bin/vcfuniq [07:34:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:34:58] Found gzip - /bin/gzip [07:34:58] Found vt - /usr/local/bin/vt [07:34:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:34:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:34:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:34:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:34:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:34:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:34:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:34:59] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:36:16] This is snippy 4.6.0
Show full stderr[07:36:16] This is snippy 4.6.0 [07:36:16] Written by Torsten Seemann [07:36:16] Obtained from https://github.com/tseemann/snippy [07:36:16] Detected operating system: linux [07:36:16] Enabling bundled linux tools. [07:36:16] Found bwa - /usr/local/bin/bwa [07:36:16] Found bcftools - /usr/local/bin/bcftools [07:36:16] Found samtools - /usr/local/bin/samtools [07:36:16] Found java - /usr/local/bin/java [07:36:16] Found snpEff - /usr/local/bin/snpEff [07:36:16] Found samclip - /usr/local/bin/samclip [07:36:16] Found seqtk - /usr/local/bin/seqtk [07:36:16] Found parallel - /usr/local/bin/parallel [07:36:16] Found freebayes - /usr/local/bin/freebayes [07:36:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:36:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:36:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:36:16] Found vcfuniq - /usr/local/bin/vcfuniq [07:36:16] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:36:16] Found gzip - /bin/gzip [07:36:16] Found vt - /usr/local/bin/vt [07:36:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:36:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:36:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:36:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:36:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:36:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:36:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:36:17] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:36:22] This is snippy 4.6.0
Show full stderr[07:36:22] This is snippy 4.6.0 [07:36:22] Written by Torsten Seemann [07:36:22] Obtained from https://github.com/tseemann/snippy [07:36:22] Detected operating system: linux [07:36:22] Enabling bundled linux tools. [07:36:22] Found bwa - /usr/local/bin/bwa [07:36:22] Found bcftools - /usr/local/bin/bcftools [07:36:22] Found samtools - /usr/local/bin/samtools [07:36:22] Found java - /usr/local/bin/java [07:36:22] Found snpEff - /usr/local/bin/snpEff [07:36:22] Found samclip - /usr/local/bin/samclip [07:36:22] Found seqtk - /usr/local/bin/seqtk [07:36:22] Found parallel - /usr/local/bin/parallel [07:36:22] Found freebayes - /usr/local/bin/freebayes [07:36:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:36:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:36:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:36:22] Found vcfuniq - /usr/local/bin/vcfuniq [07:36:22] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:36:22] Found gzip - /bin/gzip [07:36:22] Found vt - /usr/local/bin/vt [07:36:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:36:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:36:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:36:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:36:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:36:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:36:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:36:23] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:37:31] This is snippy 4.6.0
Show full stderr[07:37:31] This is snippy 4.6.0 [07:37:31] Written by Torsten Seemann [07:37:31] Obtained from https://github.com/tseemann/snippy [07:37:31] Detected operating system: linux [07:37:31] Enabling bundled linux tools. [07:37:31] Found bwa - /usr/local/bin/bwa [07:37:31] Found bcftools - /usr/local/bin/bcftools [07:37:31] Found samtools - /usr/local/bin/samtools [07:37:31] Found java - /usr/local/bin/java [07:37:31] Found snpEff - /usr/local/bin/snpEff [07:37:31] Found samclip - /usr/local/bin/samclip [07:37:31] Found seqtk - /usr/local/bin/seqtk [07:37:31] Found parallel - /usr/local/bin/parallel [07:37:31] Found freebayes - /usr/local/bin/freebayes [07:37:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:37:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:37:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:37:31] Found vcfuniq - /usr/local/bin/vcfuniq [07:37:31] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:37:31] Found gzip - /bin/gzip [07:37:31] Found vt - /usr/local/bin/vt [07:37:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:37:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:37:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:37:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:37:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:37:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:37:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:37:32] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:37:55] This is snippy 4.6.0
Show full stderr[07:37:55] This is snippy 4.6.0 [07:37:55] Written by Torsten Seemann [07:37:55] Obtained from https://github.com/tseemann/snippy [07:37:55] Detected operating system: linux [07:37:55] Enabling bundled linux tools. [07:37:55] Found bwa - /usr/local/bin/bwa [07:37:55] Found bcftools - /usr/local/bin/bcftools [07:37:55] Found samtools - /usr/local/bin/samtools [07:37:55] Found java - /usr/local/bin/java [07:37:55] Found snpEff - /usr/local/bin/snpEff [07:37:55] Found samclip - /usr/local/bin/samclip [07:37:55] Found seqtk - /usr/local/bin/seqtk [07:37:55] Found parallel - /usr/local/bin/parallel [07:37:55] Found freebayes - /usr/local/bin/freebayes [07:37:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:37:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:37:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:37:55] Found vcfuniq - /usr/local/bin/vcfuniq [07:37:55] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:37:55] Found gzip - /bin/gzip [07:37:55] Found vt - /usr/local/bin/vt [07:37:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:37:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:37:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:37:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:37:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:37:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:37:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:37:56] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:38:07] This is snippy 4.6.0
Show full stderr[07:38:07] This is snippy 4.6.0 [07:38:07] Written by Torsten Seemann [07:38:07] Obtained from https://github.com/tseemann/snippy [07:38:07] Detected operating system: linux [07:38:07] Enabling bundled linux tools. [07:38:07] Found bwa - /usr/local/bin/bwa [07:38:07] Found bcftools - /usr/local/bin/bcftools [07:38:07] Found samtools - /usr/local/bin/samtools [07:38:07] Found java - /usr/local/bin/java [07:38:07] Found snpEff - /usr/local/bin/snpEff [07:38:07] Found samclip - /usr/local/bin/samclip [07:38:07] Found seqtk - /usr/local/bin/seqtk [07:38:07] Found parallel - /usr/local/bin/parallel [07:38:07] Found freebayes - /usr/local/bin/freebayes [07:38:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:38:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:38:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:38:07] Found vcfuniq - /usr/local/bin/vcfuniq [07:38:07] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:38:07] Found gzip - /bin/gzip [07:38:07] Found vt - /usr/local/bin/vt [07:38:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:38:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:38:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:38:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:38:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:38:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:38:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:38:08] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:31:13] This is snippy 4.6.0
Show full stderr[07:31:13] This is snippy 4.6.0 [07:31:13] Written by Torsten Seemann [07:31:13] Obtained from https://github.com/tseemann/snippy [07:31:13] Detected operating system: linux [07:31:13] Enabling bundled linux tools. [07:31:13] Found bwa - /usr/local/bin/bwa [07:31:13] Found bcftools - /usr/local/bin/bcftools [07:31:13] Found samtools - /usr/local/bin/samtools [07:31:13] Found java - /usr/local/bin/java [07:31:13] Found snpEff - /usr/local/bin/snpEff [07:31:13] Found samclip - /usr/local/bin/samclip [07:31:13] Found seqtk - /usr/local/bin/seqtk [07:31:13] Found parallel - /usr/local/bin/parallel [07:31:13] Found freebayes - /usr/local/bin/freebayes [07:31:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:31:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:31:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:31:13] Found vcfuniq - /usr/local/bin/vcfuniq [07:31:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:31:13] Found gzip - /bin/gzip [07:31:13] Found vt - /usr/local/bin/vt [07:31:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:31:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:31:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:31:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:31:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:31:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:31:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:31:14] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:31:32] This is snippy 4.6.0
Show full stderr[07:31:32] This is snippy 4.6.0 [07:31:32] Written by Torsten Seemann [07:31:32] Obtained from https://github.com/tseemann/snippy [07:31:32] Detected operating system: linux [07:31:32] Enabling bundled linux tools. [07:31:32] Found bwa - /usr/local/bin/bwa [07:31:32] Found bcftools - /usr/local/bin/bcftools [07:31:32] Found samtools - /usr/local/bin/samtools [07:31:32] Found java - /usr/local/bin/java [07:31:32] Found snpEff - /usr/local/bin/snpEff [07:31:32] Found samclip - /usr/local/bin/samclip [07:31:32] Found seqtk - /usr/local/bin/seqtk [07:31:32] Found parallel - /usr/local/bin/parallel [07:31:32] Found freebayes - /usr/local/bin/freebayes [07:31:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:31:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:31:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:31:32] Found vcfuniq - /usr/local/bin/vcfuniq [07:31:32] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:31:32] Found gzip - /bin/gzip [07:31:32] Found vt - /usr/local/bin/vt [07:31:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:31:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:31:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:31:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:31:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:31:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:31:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:31:33] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:31:44] This is snippy 4.6.0
Show full stderr[07:31:44] This is snippy 4.6.0 [07:31:44] Written by Torsten Seemann [07:31:44] Obtained from https://github.com/tseemann/snippy [07:31:44] Detected operating system: linux [07:31:44] Enabling bundled linux tools. [07:31:44] Found bwa - /usr/local/bin/bwa [07:31:44] Found bcftools - /usr/local/bin/bcftools [07:31:44] Found samtools - /usr/local/bin/samtools [07:31:44] Found java - /usr/local/bin/java [07:31:44] Found snpEff - /usr/local/bin/snpEff [07:31:44] Found samclip - /usr/local/bin/samclip [07:31:44] Found seqtk - /usr/local/bin/seqtk [07:31:44] Found parallel - /usr/local/bin/parallel [07:31:44] Found freebayes - /usr/local/bin/freebayes [07:31:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:31:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:31:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:31:44] Found vcfuniq - /usr/local/bin/vcfuniq [07:31:44] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:31:44] Found gzip - /bin/gzip [07:31:44] Found vt - /usr/local/bin/vt [07:31:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:31:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:31:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:31:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:31:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:31:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:31:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:31:45] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:32:36] This is snippy 4.6.0
Show full stderr[07:32:36] This is snippy 4.6.0 [07:32:36] Written by Torsten Seemann [07:32:36] Obtained from https://github.com/tseemann/snippy [07:32:36] Detected operating system: linux [07:32:36] Enabling bundled linux tools. [07:32:36] Found bwa - /usr/local/bin/bwa [07:32:36] Found bcftools - /usr/local/bin/bcftools [07:32:36] Found samtools - /usr/local/bin/samtools [07:32:36] Found java - /usr/local/bin/java [07:32:36] Found snpEff - /usr/local/bin/snpEff [07:32:36] Found samclip - /usr/local/bin/samclip [07:32:36] Found seqtk - /usr/local/bin/seqtk [07:32:36] Found parallel - /usr/local/bin/parallel [07:32:36] Found freebayes - /usr/local/bin/freebayes [07:32:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:32:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:32:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:32:36] Found vcfuniq - /usr/local/bin/vcfuniq [07:32:36] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:32:36] Found gzip - /bin/gzip [07:32:36] Found vt - /usr/local/bin/vt [07:32:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:32:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:32:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:32:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:32:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:32:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:32:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:32:37] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:33:17] This is snippy 4.6.0
Show full stderr[07:33:17] This is snippy 4.6.0 [07:33:17] Written by Torsten Seemann [07:33:17] Obtained from https://github.com/tseemann/snippy [07:33:17] Detected operating system: linux [07:33:17] Enabling bundled linux tools. [07:33:17] Found bwa - /usr/local/bin/bwa [07:33:17] Found bcftools - /usr/local/bin/bcftools [07:33:17] Found samtools - /usr/local/bin/samtools [07:33:17] Found java - /usr/local/bin/java [07:33:17] Found snpEff - /usr/local/bin/snpEff [07:33:17] Found samclip - /usr/local/bin/samclip [07:33:17] Found seqtk - /usr/local/bin/seqtk [07:33:17] Found parallel - /usr/local/bin/parallel [07:33:17] Found freebayes - /usr/local/bin/freebayes [07:33:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:33:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:33:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:33:17] Found vcfuniq - /usr/local/bin/vcfuniq [07:33:17] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:33:17] Found gzip - /bin/gzip [07:33:17] Found vt - /usr/local/bin/vt [07:33:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:33:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:33:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:33:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:33:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:33:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:33:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:33:18] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:36:13] This is snippy 4.6.0
Show full stderr[07:36:13] This is snippy 4.6.0 [07:36:13] Written by Torsten Seemann [07:36:13] Obtained from https://github.com/tseemann/snippy [07:36:13] Detected operating system: linux [07:36:13] Enabling bundled linux tools. [07:36:13] Found bwa - /usr/local/bin/bwa [07:36:13] Found bcftools - /usr/local/bin/bcftools [07:36:13] Found samtools - /usr/local/bin/samtools [07:36:13] Found java - /usr/local/bin/java [07:36:13] Found snpEff - /usr/local/bin/snpEff [07:36:13] Found samclip - /usr/local/bin/samclip [07:36:13] Found seqtk - /usr/local/bin/seqtk [07:36:13] Found parallel - /usr/local/bin/parallel [07:36:13] Found freebayes - /usr/local/bin/freebayes [07:36:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:36:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:36:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:36:13] Found vcfuniq - /usr/local/bin/vcfuniq [07:36:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:36:13] Found gzip - /bin/gzip [07:36:13] Found vt - /usr/local/bin/vt [07:36:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:36:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:36:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:36:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:36:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:36:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:36:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:36:14] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:36:28] This is snippy 4.6.0
Show full stderr[07:36:28] This is snippy 4.6.0 [07:36:28] Written by Torsten Seemann [07:36:28] Obtained from https://github.com/tseemann/snippy [07:36:28] Detected operating system: linux [07:36:28] Enabling bundled linux tools. [07:36:28] Found bwa - /usr/local/bin/bwa [07:36:28] Found bcftools - /usr/local/bin/bcftools [07:36:28] Found samtools - /usr/local/bin/samtools [07:36:28] Found java - /usr/local/bin/java [07:36:28] Found snpEff - /usr/local/bin/snpEff [07:36:28] Found samclip - /usr/local/bin/samclip [07:36:28] Found seqtk - /usr/local/bin/seqtk [07:36:28] Found parallel - /usr/local/bin/parallel [07:36:28] Found freebayes - /usr/local/bin/freebayes [07:36:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:36:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:36:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:36:28] Found vcfuniq - /usr/local/bin/vcfuniq [07:36:28] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:36:28] Found gzip - /bin/gzip [07:36:28] Found vt - /usr/local/bin/vt [07:36:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:36:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:36:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:36:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:36:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:36:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:36:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:36:29] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:36:41] This is snippy 4.6.0
Show full stderr[07:36:41] This is snippy 4.6.0 [07:36:41] Written by Torsten Seemann [07:36:41] Obtained from https://github.com/tseemann/snippy [07:36:41] Detected operating system: linux [07:36:41] Enabling bundled linux tools. [07:36:41] Found bwa - /usr/local/bin/bwa [07:36:41] Found bcftools - /usr/local/bin/bcftools [07:36:41] Found samtools - /usr/local/bin/samtools [07:36:41] Found java - /usr/local/bin/java [07:36:41] Found snpEff - /usr/local/bin/snpEff [07:36:41] Found samclip - /usr/local/bin/samclip [07:36:41] Found seqtk - /usr/local/bin/seqtk [07:36:41] Found parallel - /usr/local/bin/parallel [07:36:41] Found freebayes - /usr/local/bin/freebayes [07:36:41] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:36:41] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:36:41] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:36:41] Found vcfuniq - /usr/local/bin/vcfuniq [07:36:41] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:36:41] Found gzip - /bin/gzip [07:36:41] Found vt - /usr/local/bin/vt [07:36:41] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:36:41] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:36:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:36:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:36:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:36:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:36:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:36:42] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:36:59] This is snippy 4.6.0
Show full stderr[07:36:59] This is snippy 4.6.0 [07:36:59] Written by Torsten Seemann [07:36:59] Obtained from https://github.com/tseemann/snippy [07:36:59] Detected operating system: linux [07:36:59] Enabling bundled linux tools. [07:36:59] Found bwa - /usr/local/bin/bwa [07:36:59] Found bcftools - /usr/local/bin/bcftools [07:36:59] Found samtools - /usr/local/bin/samtools [07:36:59] Found java - /usr/local/bin/java [07:36:59] Found snpEff - /usr/local/bin/snpEff [07:36:59] Found samclip - /usr/local/bin/samclip [07:36:59] Found seqtk - /usr/local/bin/seqtk [07:36:59] Found parallel - /usr/local/bin/parallel [07:36:59] Found freebayes - /usr/local/bin/freebayes [07:36:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:36:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:36:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:36:59] Found vcfuniq - /usr/local/bin/vcfuniq [07:36:59] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:36:59] Found gzip - /bin/gzip [07:36:59] Found vt - /usr/local/bin/vt [07:36:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:36:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:36:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:36:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:36:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:37:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:37:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:37:00] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:37:10] This is snippy 4.6.0
Show full stderr[07:37:10] This is snippy 4.6.0 [07:37:10] Written by Torsten Seemann [07:37:10] Obtained from https://github.com/tseemann/snippy [07:37:10] Detected operating system: linux [07:37:10] Enabling bundled linux tools. [07:37:10] Found bwa - /usr/local/bin/bwa [07:37:10] Found bcftools - /usr/local/bin/bcftools [07:37:10] Found samtools - /usr/local/bin/samtools [07:37:10] Found java - /usr/local/bin/java [07:37:10] Found snpEff - /usr/local/bin/snpEff [07:37:10] Found samclip - /usr/local/bin/samclip [07:37:10] Found seqtk - /usr/local/bin/seqtk [07:37:10] Found parallel - /usr/local/bin/parallel [07:37:10] Found freebayes - /usr/local/bin/freebayes [07:37:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:37:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:37:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:37:10] Found vcfuniq - /usr/local/bin/vcfuniq [07:37:10] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:37:10] Found gzip - /bin/gzip [07:37:10] Found vt - /usr/local/bin/vt [07:37:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:37:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:37:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:37:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:37:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:37:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:37:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:37:11] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:37:13] This is snippy 4.6.0
Show full stderr[07:37:13] This is snippy 4.6.0 [07:37:13] Written by Torsten Seemann [07:37:13] Obtained from https://github.com/tseemann/snippy [07:37:13] Detected operating system: linux [07:37:13] Enabling bundled linux tools. [07:37:13] Found bwa - /usr/local/bin/bwa [07:37:13] Found bcftools - /usr/local/bin/bcftools [07:37:13] Found samtools - /usr/local/bin/samtools [07:37:13] Found java - /usr/local/bin/java [07:37:13] Found snpEff - /usr/local/bin/snpEff [07:37:13] Found samclip - /usr/local/bin/samclip [07:37:13] Found seqtk - /usr/local/bin/seqtk [07:37:13] Found parallel - /usr/local/bin/parallel [07:37:13] Found freebayes - /usr/local/bin/freebayes [07:37:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:37:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:37:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:37:13] Found vcfuniq - /usr/local/bin/vcfuniq [07:37:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:37:13] Found gzip - /bin/gzip [07:37:13] Found vt - /usr/local/bin/vt [07:37:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:37:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:37:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:37:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:37:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:37:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:37:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:37:14] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:37:40] This is snippy 4.6.0
Show full stderr[07:37:40] This is snippy 4.6.0 [07:37:40] Written by Torsten Seemann [07:37:40] Obtained from https://github.com/tseemann/snippy [07:37:40] Detected operating system: linux [07:37:40] Enabling bundled linux tools. [07:37:40] Found bwa - /usr/local/bin/bwa [07:37:40] Found bcftools - /usr/local/bin/bcftools [07:37:40] Found samtools - /usr/local/bin/samtools [07:37:40] Found java - /usr/local/bin/java [07:37:40] Found snpEff - /usr/local/bin/snpEff [07:37:40] Found samclip - /usr/local/bin/samclip [07:37:40] Found seqtk - /usr/local/bin/seqtk [07:37:40] Found parallel - /usr/local/bin/parallel [07:37:40] Found freebayes - /usr/local/bin/freebayes [07:37:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:37:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:37:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:37:40] Found vcfuniq - /usr/local/bin/vcfuniq [07:37:40] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:37:40] Found gzip - /bin/gzip [07:37:40] Found vt - /usr/local/bin/vt [07:37:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:37:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:37:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:37:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:37:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:37:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:37:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:37:41] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:38:22] This is snippy 4.6.0
Show full stderr[07:38:22] This is snippy 4.6.0 [07:38:22] Written by Torsten Seemann [07:38:22] Obtained from https://github.com/tseemann/snippy [07:38:22] Detected operating system: linux [07:38:22] Enabling bundled linux tools. [07:38:22] Found bwa - /usr/local/bin/bwa [07:38:22] Found bcftools - /usr/local/bin/bcftools [07:38:22] Found samtools - /usr/local/bin/samtools [07:38:22] Found java - /usr/local/bin/java [07:38:22] Found snpEff - /usr/local/bin/snpEff [07:38:22] Found samclip - /usr/local/bin/samclip [07:38:22] Found seqtk - /usr/local/bin/seqtk [07:38:22] Found parallel - /usr/local/bin/parallel [07:38:22] Found freebayes - /usr/local/bin/freebayes [07:38:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:38:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:38:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:38:22] Found vcfuniq - /usr/local/bin/vcfuniq [07:38:22] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:38:22] Found gzip - /bin/gzip [07:38:22] Found vt - /usr/local/bin/vt [07:38:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:38:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:38:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:38:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:38:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:38:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:38:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:38:23] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:35:27] This is snippy 4.6.0
Show full stderr[07:35:27] This is snippy 4.6.0 [07:35:27] Written by Torsten Seemann [07:35:27] Obtained from https://github.com/tseemann/snippy [07:35:27] Detected operating system: linux [07:35:27] Enabling bundled linux tools. [07:35:27] Found bwa - /usr/local/bin/bwa [07:35:27] Found bcftools - /usr/local/bin/bcftools [07:35:27] Found samtools - /usr/local/bin/samtools [07:35:27] Found java - /usr/local/bin/java [07:35:27] Found snpEff - /usr/local/bin/snpEff [07:35:27] Found samclip - /usr/local/bin/samclip [07:35:27] Found seqtk - /usr/local/bin/seqtk [07:35:27] Found parallel - /usr/local/bin/parallel [07:35:27] Found freebayes - /usr/local/bin/freebayes [07:35:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:35:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:35:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:35:27] Found vcfuniq - /usr/local/bin/vcfuniq [07:35:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:35:27] Found gzip - /bin/gzip [07:35:27] Found vt - /usr/local/bin/vt [07:35:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:35:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:35:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:35:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:35:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:35:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:35:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:35:28] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:36:00] This is snippy 4.6.0
Show full stderr[07:36:00] This is snippy 4.6.0 [07:36:00] Written by Torsten Seemann [07:36:00] Obtained from https://github.com/tseemann/snippy [07:36:00] Detected operating system: linux [07:36:00] Enabling bundled linux tools. [07:36:00] Found bwa - /usr/local/bin/bwa [07:36:00] Found bcftools - /usr/local/bin/bcftools [07:36:00] Found samtools - /usr/local/bin/samtools [07:36:00] Found java - /usr/local/bin/java [07:36:00] Found snpEff - /usr/local/bin/snpEff [07:36:00] Found samclip - /usr/local/bin/samclip [07:36:00] Found seqtk - /usr/local/bin/seqtk [07:36:00] Found parallel - /usr/local/bin/parallel [07:36:00] Found freebayes - /usr/local/bin/freebayes [07:36:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:36:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:36:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:36:00] Found vcfuniq - /usr/local/bin/vcfuniq [07:36:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:36:00] Found gzip - /bin/gzip [07:36:00] Found vt - /usr/local/bin/vt [07:36:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:36:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:36:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:36:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:36:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:36:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:36:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:36:01] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:36:03] This is snippy 4.6.0
Show full stderr[07:36:03] This is snippy 4.6.0 [07:36:03] Written by Torsten Seemann [07:36:03] Obtained from https://github.com/tseemann/snippy [07:36:03] Detected operating system: linux [07:36:03] Enabling bundled linux tools. [07:36:03] Found bwa - /usr/local/bin/bwa [07:36:03] Found bcftools - /usr/local/bin/bcftools [07:36:03] Found samtools - /usr/local/bin/samtools [07:36:03] Found java - /usr/local/bin/java [07:36:03] Found snpEff - /usr/local/bin/snpEff [07:36:03] Found samclip - /usr/local/bin/samclip [07:36:03] Found seqtk - /usr/local/bin/seqtk [07:36:03] Found parallel - /usr/local/bin/parallel [07:36:03] Found freebayes - /usr/local/bin/freebayes [07:36:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:36:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:36:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:36:03] Found vcfuniq - /usr/local/bin/vcfuniq [07:36:03] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:36:03] Found gzip - /bin/gzip [07:36:03] Found vt - /usr/local/bin/vt [07:36:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:36:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:36:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:36:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:36:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:36:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:36:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:36:04] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:37:25] This is snippy 4.6.0
Show full stderr[07:37:25] This is snippy 4.6.0 [07:37:25] Written by Torsten Seemann [07:37:25] Obtained from https://github.com/tseemann/snippy [07:37:25] Detected operating system: linux [07:37:25] Enabling bundled linux tools. [07:37:25] Found bwa - /usr/local/bin/bwa [07:37:25] Found bcftools - /usr/local/bin/bcftools [07:37:25] Found samtools - /usr/local/bin/samtools [07:37:25] Found java - /usr/local/bin/java [07:37:25] Found snpEff - /usr/local/bin/snpEff [07:37:25] Found samclip - /usr/local/bin/samclip [07:37:25] Found seqtk - /usr/local/bin/seqtk [07:37:25] Found parallel - /usr/local/bin/parallel [07:37:25] Found freebayes - /usr/local/bin/freebayes [07:37:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:37:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:37:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:37:25] Found vcfuniq - /usr/local/bin/vcfuniq [07:37:25] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:37:25] Found gzip - /bin/gzip [07:37:25] Found vt - /usr/local/bin/vt [07:37:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:37:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:37:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:37:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:37:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:37:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:37:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:37:26] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:38:36] This is snippy 4.6.0
Show full stderr[07:38:36] This is snippy 4.6.0 [07:38:36] Written by Torsten Seemann [07:38:36] Obtained from https://github.com/tseemann/snippy [07:38:36] Detected operating system: linux [07:38:36] Enabling bundled linux tools. [07:38:36] Found bwa - /usr/local/bin/bwa [07:38:36] Found bcftools - /usr/local/bin/bcftools [07:38:36] Found samtools - /usr/local/bin/samtools [07:38:36] Found java - /usr/local/bin/java [07:38:36] Found snpEff - /usr/local/bin/snpEff [07:38:36] Found samclip - /usr/local/bin/samclip [07:38:36] Found seqtk - /usr/local/bin/seqtk [07:38:36] Found parallel - /usr/local/bin/parallel [07:38:36] Found freebayes - /usr/local/bin/freebayes [07:38:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:38:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:38:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:38:36] Found vcfuniq - /usr/local/bin/vcfuniq [07:38:36] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:38:36] Found gzip - /bin/gzip [07:38:36] Found vt - /usr/local/bin/vt [07:38:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:38:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:38:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:38:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:38:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:38:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:38:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:38:37] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:38:57] This is snippy 4.6.0
Show full stderr[07:38:57] This is snippy 4.6.0 [07:38:57] Written by Torsten Seemann [07:38:57] Obtained from https://github.com/tseemann/snippy [07:38:57] Detected operating system: linux [07:38:57] Enabling bundled linux tools. [07:38:57] Found bwa - /usr/local/bin/bwa [07:38:57] Found bcftools - /usr/local/bin/bcftools [07:38:58] Found samtools - /usr/local/bin/samtools [07:38:58] Found java - /usr/local/bin/java [07:38:58] Found snpEff - /usr/local/bin/snpEff [07:38:58] Found samclip - /usr/local/bin/samclip [07:38:58] Found seqtk - /usr/local/bin/seqtk [07:38:58] Found parallel - /usr/local/bin/parallel [07:38:58] Found freebayes - /usr/local/bin/freebayes [07:38:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:38:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:38:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:38:58] Found vcfuniq - /usr/local/bin/vcfuniq [07:38:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:38:58] Found gzip - /bin/gzip [07:38:58] Found vt - /usr/local/bin/vt [07:38:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:38:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:38:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:38:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:38:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:38:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:38:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:38:58] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:40:44] This is snippy 4.6.0
Show full stderr[07:40:44] This is snippy 4.6.0 [07:40:44] Written by Torsten Seemann [07:40:44] Obtained from https://github.com/tseemann/snippy [07:40:44] Detected operating system: linux [07:40:44] Enabling bundled linux tools. [07:40:44] Found bwa - /usr/local/bin/bwa [07:40:44] Found bcftools - /usr/local/bin/bcftools [07:40:44] Found samtools - /usr/local/bin/samtools [07:40:44] Found java - /usr/local/bin/java [07:40:44] Found snpEff - /usr/local/bin/snpEff [07:40:44] Found samclip - /usr/local/bin/samclip [07:40:44] Found seqtk - /usr/local/bin/seqtk [07:40:44] Found parallel - /usr/local/bin/parallel [07:40:44] Found freebayes - /usr/local/bin/freebayes [07:40:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:40:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:40:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:40:44] Found vcfuniq - /usr/local/bin/vcfuniq [07:40:44] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:40:44] Found gzip - /bin/gzip [07:40:44] Found vt - /usr/local/bin/vt [07:40:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:40:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:40:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:40:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:40:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:40:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:40:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:40:44] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:39:51] This is snippy 4.6.0
Show full stderr[07:39:51] This is snippy 4.6.0 [07:39:51] Written by Torsten Seemann [07:39:51] Obtained from https://github.com/tseemann/snippy [07:39:51] Detected operating system: linux [07:39:51] Enabling bundled linux tools. [07:39:51] Found bwa - /usr/local/bin/bwa [07:39:51] Found bcftools - /usr/local/bin/bcftools [07:39:51] Found samtools - /usr/local/bin/samtools [07:39:51] Found java - /usr/local/bin/java [07:39:51] Found snpEff - /usr/local/bin/snpEff [07:39:51] Found samclip - /usr/local/bin/samclip [07:39:51] Found seqtk - /usr/local/bin/seqtk [07:39:51] Found parallel - /usr/local/bin/parallel [07:39:51] Found freebayes - /usr/local/bin/freebayes [07:39:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:39:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:39:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:39:51] Found vcfuniq - /usr/local/bin/vcfuniq [07:39:51] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:39:51] Found gzip - /bin/gzip [07:39:51] Found vt - /usr/local/bin/vt [07:39:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:39:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:39:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:39:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:39:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:39:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:39:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:39:51] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:40:03] This is snippy 4.6.0
Show full stderr[07:40:03] This is snippy 4.6.0 [07:40:03] Written by Torsten Seemann [07:40:03] Obtained from https://github.com/tseemann/snippy [07:40:03] Detected operating system: linux [07:40:03] Enabling bundled linux tools. [07:40:03] Found bwa - /usr/local/bin/bwa [07:40:03] Found bcftools - /usr/local/bin/bcftools [07:40:03] Found samtools - /usr/local/bin/samtools [07:40:03] Found java - /usr/local/bin/java [07:40:03] Found snpEff - /usr/local/bin/snpEff [07:40:03] Found samclip - /usr/local/bin/samclip [07:40:03] Found seqtk - /usr/local/bin/seqtk [07:40:03] Found parallel - /usr/local/bin/parallel [07:40:03] Found freebayes - /usr/local/bin/freebayes [07:40:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:40:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:40:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:40:04] Found vcfuniq - /usr/local/bin/vcfuniq [07:40:04] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:40:04] Found gzip - /bin/gzip [07:40:04] Found vt - /usr/local/bin/vt [07:40:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:40:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:40:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:40:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:40:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:40:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:40:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:40:04] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:40:15] This is snippy 4.6.0
Show full stderr[07:40:15] This is snippy 4.6.0 [07:40:15] Written by Torsten Seemann [07:40:15] Obtained from https://github.com/tseemann/snippy [07:40:15] Detected operating system: linux [07:40:15] Enabling bundled linux tools. [07:40:15] Found bwa - /usr/local/bin/bwa [07:40:15] Found bcftools - /usr/local/bin/bcftools [07:40:15] Found samtools - /usr/local/bin/samtools [07:40:15] Found java - /usr/local/bin/java [07:40:15] Found snpEff - /usr/local/bin/snpEff [07:40:15] Found samclip - /usr/local/bin/samclip [07:40:15] Found seqtk - /usr/local/bin/seqtk [07:40:15] Found parallel - /usr/local/bin/parallel [07:40:15] Found freebayes - /usr/local/bin/freebayes [07:40:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:40:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:40:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:40:15] Found vcfuniq - /usr/local/bin/vcfuniq [07:40:16] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:40:16] Found gzip - /bin/gzip [07:40:16] Found vt - /usr/local/bin/vt [07:40:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:40:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:40:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:40:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:40:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:40:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:40:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:40:16] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:40:58] This is snippy 4.6.0
Show full stderr[07:40:58] This is snippy 4.6.0 [07:40:58] Written by Torsten Seemann [07:40:58] Obtained from https://github.com/tseemann/snippy [07:40:58] Detected operating system: linux [07:40:58] Enabling bundled linux tools. [07:40:58] Found bwa - /usr/local/bin/bwa [07:40:58] Found bcftools - /usr/local/bin/bcftools [07:40:58] Found samtools - /usr/local/bin/samtools [07:40:58] Found java - /usr/local/bin/java [07:40:58] Found snpEff - /usr/local/bin/snpEff [07:40:58] Found samclip - /usr/local/bin/samclip [07:40:58] Found seqtk - /usr/local/bin/seqtk [07:40:58] Found parallel - /usr/local/bin/parallel [07:40:58] Found freebayes - /usr/local/bin/freebayes [07:40:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:40:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:40:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:40:58] Found vcfuniq - /usr/local/bin/vcfuniq [07:40:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:40:58] Found gzip - /bin/gzip [07:40:58] Found vt - /usr/local/bin/vt [07:40:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:40:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:40:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:40:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:40:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:40:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:40:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:40:58] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:42:22] This is snippy 4.6.0
Show full stderr[07:42:22] This is snippy 4.6.0 [07:42:22] Written by Torsten Seemann [07:42:22] Obtained from https://github.com/tseemann/snippy [07:42:22] Detected operating system: linux [07:42:22] Enabling bundled linux tools. [07:42:22] Found bwa - /usr/local/bin/bwa [07:42:22] Found bcftools - /usr/local/bin/bcftools [07:42:22] Found samtools - /usr/local/bin/samtools [07:42:22] Found java - /usr/local/bin/java [07:42:22] Found snpEff - /usr/local/bin/snpEff [07:42:22] Found samclip - /usr/local/bin/samclip [07:42:22] Found seqtk - /usr/local/bin/seqtk [07:42:22] Found parallel - /usr/local/bin/parallel [07:42:22] Found freebayes - /usr/local/bin/freebayes [07:42:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:42:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:42:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:42:22] Found vcfuniq - /usr/local/bin/vcfuniq [07:42:22] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:42:22] Found gzip - /bin/gzip [07:42:22] Found vt - /usr/local/bin/vt [07:42:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:42:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:42:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:42:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:42:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:42:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:42:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:42:23] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:42:28] This is snippy 4.6.0
Show full stderr[07:42:28] This is snippy 4.6.0 [07:42:28] Written by Torsten Seemann [07:42:28] Obtained from https://github.com/tseemann/snippy [07:42:28] Detected operating system: linux [07:42:28] Enabling bundled linux tools. [07:42:28] Found bwa - /usr/local/bin/bwa [07:42:28] Found bcftools - /usr/local/bin/bcftools [07:42:28] Found samtools - /usr/local/bin/samtools [07:42:28] Found java - /usr/local/bin/java [07:42:28] Found snpEff - /usr/local/bin/snpEff [07:42:28] Found samclip - /usr/local/bin/samclip [07:42:28] Found seqtk - /usr/local/bin/seqtk [07:42:28] Found parallel - /usr/local/bin/parallel [07:42:28] Found freebayes - /usr/local/bin/freebayes [07:42:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:42:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:42:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:42:28] Found vcfuniq - /usr/local/bin/vcfuniq [07:42:28] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:42:28] Found gzip - /bin/gzip [07:42:28] Found vt - /usr/local/bin/vt [07:42:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:42:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:42:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:42:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:42:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:42:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:42:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:42:29] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:42:31] This is snippy 4.6.0
Show full stderr[07:42:31] This is snippy 4.6.0 [07:42:31] Written by Torsten Seemann [07:42:31] Obtained from https://github.com/tseemann/snippy [07:42:31] Detected operating system: linux [07:42:31] Enabling bundled linux tools. [07:42:31] Found bwa - /usr/local/bin/bwa [07:42:31] Found bcftools - /usr/local/bin/bcftools [07:42:31] Found samtools - /usr/local/bin/samtools [07:42:31] Found java - /usr/local/bin/java [07:42:31] Found snpEff - /usr/local/bin/snpEff [07:42:31] Found samclip - /usr/local/bin/samclip [07:42:31] Found seqtk - /usr/local/bin/seqtk [07:42:31] Found parallel - /usr/local/bin/parallel [07:42:31] Found freebayes - /usr/local/bin/freebayes [07:42:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:42:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:42:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:42:31] Found vcfuniq - /usr/local/bin/vcfuniq [07:42:31] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:42:31] Found gzip - /bin/gzip [07:42:31] Found vt - /usr/local/bin/vt [07:42:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:42:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:42:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:42:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:42:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:42:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:42:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:42:31] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:34:28] This is snippy 4.6.0
Show full stderr[07:34:28] This is snippy 4.6.0 [07:34:28] Written by Torsten Seemann [07:34:28] Obtained from https://github.com/tseemann/snippy [07:34:28] Detected operating system: linux [07:34:28] Enabling bundled linux tools. [07:34:28] Found bwa - /usr/local/bin/bwa [07:34:28] Found bcftools - /usr/local/bin/bcftools [07:34:28] Found samtools - /usr/local/bin/samtools [07:34:28] Found java - /usr/local/bin/java [07:34:28] Found snpEff - /usr/local/bin/snpEff [07:34:28] Found samclip - /usr/local/bin/samclip [07:34:28] Found seqtk - /usr/local/bin/seqtk [07:34:28] Found parallel - /usr/local/bin/parallel [07:34:28] Found freebayes - /usr/local/bin/freebayes [07:34:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:34:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:34:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:34:28] Found vcfuniq - /usr/local/bin/vcfuniq [07:34:28] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:34:28] Found gzip - /bin/gzip [07:34:28] Found vt - /usr/local/bin/vt [07:34:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:34:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:34:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:34:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:34:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:34:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:34:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:34:29] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:35:45] This is snippy 4.6.0
Show full stderr[07:35:45] This is snippy 4.6.0 [07:35:45] Written by Torsten Seemann [07:35:45] Obtained from https://github.com/tseemann/snippy [07:35:45] Detected operating system: linux [07:35:45] Enabling bundled linux tools. [07:35:45] Found bwa - /usr/local/bin/bwa [07:35:45] Found bcftools - /usr/local/bin/bcftools [07:35:45] Found samtools - /usr/local/bin/samtools [07:35:45] Found java - /usr/local/bin/java [07:35:45] Found snpEff - /usr/local/bin/snpEff [07:35:45] Found samclip - /usr/local/bin/samclip [07:35:45] Found seqtk - /usr/local/bin/seqtk [07:35:45] Found parallel - /usr/local/bin/parallel [07:35:45] Found freebayes - /usr/local/bin/freebayes [07:35:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:35:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:35:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:35:45] Found vcfuniq - /usr/local/bin/vcfuniq [07:35:45] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:35:45] Found gzip - /bin/gzip [07:35:45] Found vt - /usr/local/bin/vt [07:35:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:35:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:35:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:35:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:35:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:35:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:35:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:35:46] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:36:07] This is snippy 4.6.0
Show full stderr[07:36:07] This is snippy 4.6.0 [07:36:07] Written by Torsten Seemann [07:36:07] Obtained from https://github.com/tseemann/snippy [07:36:07] Detected operating system: linux [07:36:07] Enabling bundled linux tools. [07:36:07] Found bwa - /usr/local/bin/bwa [07:36:07] Found bcftools - /usr/local/bin/bcftools [07:36:07] Found samtools - /usr/local/bin/samtools [07:36:07] Found java - /usr/local/bin/java [07:36:07] Found snpEff - /usr/local/bin/snpEff [07:36:07] Found samclip - /usr/local/bin/samclip [07:36:07] Found seqtk - /usr/local/bin/seqtk [07:36:07] Found parallel - /usr/local/bin/parallel [07:36:07] Found freebayes - /usr/local/bin/freebayes [07:36:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:36:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:36:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:36:07] Found vcfuniq - /usr/local/bin/vcfuniq [07:36:07] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:36:07] Found gzip - /bin/gzip [07:36:07] Found vt - /usr/local/bin/vt [07:36:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:36:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:36:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:36:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:36:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:36:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:36:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:36:08] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:36:19] This is snippy 4.6.0
Show full stderr[07:36:19] This is snippy 4.6.0 [07:36:19] Written by Torsten Seemann [07:36:19] Obtained from https://github.com/tseemann/snippy [07:36:19] Detected operating system: linux [07:36:19] Enabling bundled linux tools. [07:36:19] Found bwa - /usr/local/bin/bwa [07:36:19] Found bcftools - /usr/local/bin/bcftools [07:36:19] Found samtools - /usr/local/bin/samtools [07:36:19] Found java - /usr/local/bin/java [07:36:19] Found snpEff - /usr/local/bin/snpEff [07:36:19] Found samclip - /usr/local/bin/samclip [07:36:19] Found seqtk - /usr/local/bin/seqtk [07:36:19] Found parallel - /usr/local/bin/parallel [07:36:19] Found freebayes - /usr/local/bin/freebayes [07:36:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:36:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:36:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:36:19] Found vcfuniq - /usr/local/bin/vcfuniq [07:36:19] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:36:19] Found gzip - /bin/gzip [07:36:19] Found vt - /usr/local/bin/vt [07:36:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:36:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:36:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:36:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:36:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:36:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:36:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:36:20] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:36:31] This is snippy 4.6.0
Show full stderr[07:36:31] This is snippy 4.6.0 [07:36:31] Written by Torsten Seemann [07:36:31] Obtained from https://github.com/tseemann/snippy [07:36:31] Detected operating system: linux [07:36:31] Enabling bundled linux tools. [07:36:31] Found bwa - /usr/local/bin/bwa [07:36:31] Found bcftools - /usr/local/bin/bcftools [07:36:31] Found samtools - /usr/local/bin/samtools [07:36:31] Found java - /usr/local/bin/java [07:36:31] Found snpEff - /usr/local/bin/snpEff [07:36:31] Found samclip - /usr/local/bin/samclip [07:36:31] Found seqtk - /usr/local/bin/seqtk [07:36:31] Found parallel - /usr/local/bin/parallel [07:36:31] Found freebayes - /usr/local/bin/freebayes [07:36:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:36:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:36:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:36:31] Found vcfuniq - /usr/local/bin/vcfuniq [07:36:31] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:36:31] Found gzip - /bin/gzip [07:36:31] Found vt - /usr/local/bin/vt [07:36:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:36:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:36:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:36:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:36:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:36:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:36:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:36:32] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:36:44] This is snippy 4.6.0
Show full stderr[07:36:44] This is snippy 4.6.0 [07:36:44] Written by Torsten Seemann [07:36:44] Obtained from https://github.com/tseemann/snippy [07:36:44] Detected operating system: linux [07:36:44] Enabling bundled linux tools. [07:36:44] Found bwa - /usr/local/bin/bwa [07:36:44] Found bcftools - /usr/local/bin/bcftools [07:36:44] Found samtools - /usr/local/bin/samtools [07:36:44] Found java - /usr/local/bin/java [07:36:44] Found snpEff - /usr/local/bin/snpEff [07:36:44] Found samclip - /usr/local/bin/samclip [07:36:44] Found seqtk - /usr/local/bin/seqtk [07:36:44] Found parallel - /usr/local/bin/parallel [07:36:44] Found freebayes - /usr/local/bin/freebayes [07:36:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:36:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:36:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:36:44] Found vcfuniq - /usr/local/bin/vcfuniq [07:36:44] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:36:44] Found gzip - /bin/gzip [07:36:44] Found vt - /usr/local/bin/vt [07:36:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:36:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:36:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:36:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:36:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:36:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:36:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:36:45] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:36:56] This is snippy 4.6.0
Show full stderr[07:36:56] This is snippy 4.6.0 [07:36:56] Written by Torsten Seemann [07:36:56] Obtained from https://github.com/tseemann/snippy [07:36:56] Detected operating system: linux [07:36:56] Enabling bundled linux tools. [07:36:56] Found bwa - /usr/local/bin/bwa [07:36:56] Found bcftools - /usr/local/bin/bcftools [07:36:56] Found samtools - /usr/local/bin/samtools [07:36:56] Found java - /usr/local/bin/java [07:36:56] Found snpEff - /usr/local/bin/snpEff [07:36:56] Found samclip - /usr/local/bin/samclip [07:36:56] Found seqtk - /usr/local/bin/seqtk [07:36:56] Found parallel - /usr/local/bin/parallel [07:36:56] Found freebayes - /usr/local/bin/freebayes [07:36:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:36:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:36:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:36:56] Found vcfuniq - /usr/local/bin/vcfuniq [07:36:56] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:36:56] Found gzip - /bin/gzip [07:36:56] Found vt - /usr/local/bin/vt [07:36:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:36:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:36:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:36:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:36:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:36:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:36:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:36:57] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:38:42] This is snippy 4.6.0
Show full stderr[07:38:42] This is snippy 4.6.0 [07:38:42] Written by Torsten Seemann [07:38:42] Obtained from https://github.com/tseemann/snippy [07:38:42] Detected operating system: linux [07:38:42] Enabling bundled linux tools. [07:38:42] Found bwa - /usr/local/bin/bwa [07:38:42] Found bcftools - /usr/local/bin/bcftools [07:38:42] Found samtools - /usr/local/bin/samtools [07:38:42] Found java - /usr/local/bin/java [07:38:42] Found snpEff - /usr/local/bin/snpEff [07:38:42] Found samclip - /usr/local/bin/samclip [07:38:42] Found seqtk - /usr/local/bin/seqtk [07:38:42] Found parallel - /usr/local/bin/parallel [07:38:42] Found freebayes - /usr/local/bin/freebayes [07:38:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:38:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:38:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:38:42] Found vcfuniq - /usr/local/bin/vcfuniq [07:38:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:38:42] Found gzip - /bin/gzip [07:38:42] Found vt - /usr/local/bin/vt [07:38:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:38:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:38:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:38:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:38:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:38:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:38:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:38:43] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:38:51] This is snippy 4.6.0
Show full stderr[07:38:51] This is snippy 4.6.0 [07:38:51] Written by Torsten Seemann [07:38:51] Obtained from https://github.com/tseemann/snippy [07:38:51] Detected operating system: linux [07:38:51] Enabling bundled linux tools. [07:38:51] Found bwa - /usr/local/bin/bwa [07:38:51] Found bcftools - /usr/local/bin/bcftools [07:38:51] Found samtools - /usr/local/bin/samtools [07:38:51] Found java - /usr/local/bin/java [07:38:51] Found snpEff - /usr/local/bin/snpEff [07:38:51] Found samclip - /usr/local/bin/samclip [07:38:51] Found seqtk - /usr/local/bin/seqtk [07:38:51] Found parallel - /usr/local/bin/parallel [07:38:51] Found freebayes - /usr/local/bin/freebayes [07:38:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:38:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:38:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:38:51] Found vcfuniq - /usr/local/bin/vcfuniq [07:38:51] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:38:51] Found gzip - /bin/gzip [07:38:51] Found vt - /usr/local/bin/vt [07:38:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:38:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:38:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:38:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:38:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:38:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:38:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:38:52] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:39:10] This is snippy 4.6.0
Show full stderr[07:39:10] This is snippy 4.6.0 [07:39:10] Written by Torsten Seemann [07:39:10] Obtained from https://github.com/tseemann/snippy [07:39:10] Detected operating system: linux [07:39:10] Enabling bundled linux tools. [07:39:10] Found bwa - /usr/local/bin/bwa [07:39:10] Found bcftools - /usr/local/bin/bcftools [07:39:10] Found samtools - /usr/local/bin/samtools [07:39:10] Found java - /usr/local/bin/java [07:39:10] Found snpEff - /usr/local/bin/snpEff [07:39:10] Found samclip - /usr/local/bin/samclip [07:39:10] Found seqtk - /usr/local/bin/seqtk [07:39:10] Found parallel - /usr/local/bin/parallel [07:39:10] Found freebayes - /usr/local/bin/freebayes [07:39:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:39:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:39:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:39:10] Found vcfuniq - /usr/local/bin/vcfuniq [07:39:10] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:39:10] Found gzip - /bin/gzip [07:39:10] Found vt - /usr/local/bin/vt [07:39:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:39:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:39:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:39:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:39:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:39:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:39:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:39:10] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:39:40] This is snippy 4.6.0
Show full stderr[07:39:40] This is snippy 4.6.0 [07:39:40] Written by Torsten Seemann [07:39:40] Obtained from https://github.com/tseemann/snippy [07:39:40] Detected operating system: linux [07:39:40] Enabling bundled linux tools. [07:39:40] Found bwa - /usr/local/bin/bwa [07:39:40] Found bcftools - /usr/local/bin/bcftools [07:39:40] Found samtools - /usr/local/bin/samtools [07:39:40] Found java - /usr/local/bin/java [07:39:40] Found snpEff - /usr/local/bin/snpEff [07:39:40] Found samclip - /usr/local/bin/samclip [07:39:40] Found seqtk - /usr/local/bin/seqtk [07:39:40] Found parallel - /usr/local/bin/parallel [07:39:41] Found freebayes - /usr/local/bin/freebayes [07:39:41] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:39:41] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:39:41] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:39:41] Found vcfuniq - /usr/local/bin/vcfuniq [07:39:41] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:39:41] Found gzip - /bin/gzip [07:39:41] Found vt - /usr/local/bin/vt [07:39:41] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:39:41] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:39:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:39:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:39:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:39:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:39:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:39:41] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:39:56] This is snippy 4.6.0
Show full stderr[07:39:56] This is snippy 4.6.0 [07:39:56] Written by Torsten Seemann [07:39:56] Obtained from https://github.com/tseemann/snippy [07:39:56] Detected operating system: linux [07:39:56] Enabling bundled linux tools. [07:39:56] Found bwa - /usr/local/bin/bwa [07:39:56] Found bcftools - /usr/local/bin/bcftools [07:39:56] Found samtools - /usr/local/bin/samtools [07:39:56] Found java - /usr/local/bin/java [07:39:56] Found snpEff - /usr/local/bin/snpEff [07:39:56] Found samclip - /usr/local/bin/samclip [07:39:56] Found seqtk - /usr/local/bin/seqtk [07:39:56] Found parallel - /usr/local/bin/parallel [07:39:56] Found freebayes - /usr/local/bin/freebayes [07:39:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:39:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:39:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:39:57] Found vcfuniq - /usr/local/bin/vcfuniq [07:39:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:39:57] Found gzip - /bin/gzip [07:39:57] Found vt - /usr/local/bin/vt [07:39:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:39:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:39:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:39:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:39:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:39:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:39:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:39:57] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:40:10] This is snippy 4.6.0
Show full stderr[07:40:10] This is snippy 4.6.0 [07:40:10] Written by Torsten Seemann [07:40:10] Obtained from https://github.com/tseemann/snippy [07:40:10] Detected operating system: linux [07:40:10] Enabling bundled linux tools. [07:40:10] Found bwa - /usr/local/bin/bwa [07:40:10] Found bcftools - /usr/local/bin/bcftools [07:40:10] Found samtools - /usr/local/bin/samtools [07:40:10] Found java - /usr/local/bin/java [07:40:10] Found snpEff - /usr/local/bin/snpEff [07:40:10] Found samclip - /usr/local/bin/samclip [07:40:10] Found seqtk - /usr/local/bin/seqtk [07:40:10] Found parallel - /usr/local/bin/parallel [07:40:10] Found freebayes - /usr/local/bin/freebayes [07:40:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:40:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:40:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:40:10] Found vcfuniq - /usr/local/bin/vcfuniq [07:40:10] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:40:10] Found gzip - /bin/gzip [07:40:10] Found vt - /usr/local/bin/vt [07:40:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:40:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:40:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:40:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:40:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:40:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:40:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:40:11] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:40:30] This is snippy 4.6.0
Show full stderr[07:40:30] This is snippy 4.6.0 [07:40:30] Written by Torsten Seemann [07:40:30] Obtained from https://github.com/tseemann/snippy [07:40:30] Detected operating system: linux [07:40:30] Enabling bundled linux tools. [07:40:30] Found bwa - /usr/local/bin/bwa [07:40:30] Found bcftools - /usr/local/bin/bcftools [07:40:30] Found samtools - /usr/local/bin/samtools [07:40:30] Found java - /usr/local/bin/java [07:40:30] Found snpEff - /usr/local/bin/snpEff [07:40:30] Found samclip - /usr/local/bin/samclip [07:40:30] Found seqtk - /usr/local/bin/seqtk [07:40:30] Found parallel - /usr/local/bin/parallel [07:40:30] Found freebayes - /usr/local/bin/freebayes [07:40:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:40:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:40:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:40:30] Found vcfuniq - /usr/local/bin/vcfuniq [07:40:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:40:30] Found gzip - /bin/gzip [07:40:30] Found vt - /usr/local/bin/vt [07:40:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:40:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:40:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:40:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:40:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:40:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:40:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:40:31] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:42:37] This is snippy 4.6.0
Show full stderr[07:42:37] This is snippy 4.6.0 [07:42:37] Written by Torsten Seemann [07:42:37] Obtained from https://github.com/tseemann/snippy [07:42:37] Detected operating system: linux [07:42:37] Enabling bundled linux tools. [07:42:37] Found bwa - /usr/local/bin/bwa [07:42:37] Found bcftools - /usr/local/bin/bcftools [07:42:37] Found samtools - /usr/local/bin/samtools [07:42:37] Found java - /usr/local/bin/java [07:42:37] Found snpEff - /usr/local/bin/snpEff [07:42:37] Found samclip - /usr/local/bin/samclip [07:42:37] Found seqtk - /usr/local/bin/seqtk [07:42:37] Found parallel - /usr/local/bin/parallel [07:42:37] Found freebayes - /usr/local/bin/freebayes [07:42:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:42:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:42:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:42:37] Found vcfuniq - /usr/local/bin/vcfuniq [07:42:37] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:42:37] Found gzip - /bin/gzip [07:42:37] Found vt - /usr/local/bin/vt [07:42:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:42:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:42:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:42:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:42:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:42:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:42:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:42:38] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:43:01] This is snippy 4.6.0
Show full stderr[07:43:01] This is snippy 4.6.0 [07:43:01] Written by Torsten Seemann [07:43:01] Obtained from https://github.com/tseemann/snippy [07:43:01] Detected operating system: linux [07:43:01] Enabling bundled linux tools. [07:43:01] Found bwa - /usr/local/bin/bwa [07:43:01] Found bcftools - /usr/local/bin/bcftools [07:43:01] Found samtools - /usr/local/bin/samtools [07:43:01] Found java - /usr/local/bin/java [07:43:01] Found snpEff - /usr/local/bin/snpEff [07:43:01] Found samclip - /usr/local/bin/samclip [07:43:01] Found seqtk - /usr/local/bin/seqtk [07:43:01] Found parallel - /usr/local/bin/parallel [07:43:01] Found freebayes - /usr/local/bin/freebayes [07:43:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:43:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:43:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:43:01] Found vcfuniq - /usr/local/bin/vcfuniq [07:43:01] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:43:01] Found gzip - /bin/gzip [07:43:01] Found vt - /usr/local/bin/vt [07:43:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:43:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:43:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:43:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:43:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:43:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:43:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:43:02] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:43:16] This is snippy 4.6.0
Show full stderr[07:43:16] This is snippy 4.6.0 [07:43:16] Written by Torsten Seemann [07:43:16] Obtained from https://github.com/tseemann/snippy [07:43:16] Detected operating system: linux [07:43:16] Enabling bundled linux tools. [07:43:16] Found bwa - /usr/local/bin/bwa [07:43:16] Found bcftools - /usr/local/bin/bcftools [07:43:16] Found samtools - /usr/local/bin/samtools [07:43:16] Found java - /usr/local/bin/java [07:43:16] Found snpEff - /usr/local/bin/snpEff [07:43:16] Found samclip - /usr/local/bin/samclip [07:43:16] Found seqtk - /usr/local/bin/seqtk [07:43:16] Found parallel - /usr/local/bin/parallel [07:43:16] Found freebayes - /usr/local/bin/freebayes [07:43:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:43:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:43:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:43:16] Found vcfuniq - /usr/local/bin/vcfuniq [07:43:16] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:43:16] Found gzip - /bin/gzip [07:43:16] Found vt - /usr/local/bin/vt [07:43:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:43:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:43:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:43:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:43:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:43:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:43:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:43:17] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:43:35] This is snippy 4.6.0
Show full stderr[07:43:35] This is snippy 4.6.0 [07:43:35] Written by Torsten Seemann [07:43:35] Obtained from https://github.com/tseemann/snippy [07:43:35] Detected operating system: linux [07:43:35] Enabling bundled linux tools. [07:43:35] Found bwa - /usr/local/bin/bwa [07:43:35] Found bcftools - /usr/local/bin/bcftools [07:43:35] Found samtools - /usr/local/bin/samtools [07:43:35] Found java - /usr/local/bin/java [07:43:35] Found snpEff - /usr/local/bin/snpEff [07:43:35] Found samclip - /usr/local/bin/samclip [07:43:35] Found seqtk - /usr/local/bin/seqtk [07:43:35] Found parallel - /usr/local/bin/parallel [07:43:35] Found freebayes - /usr/local/bin/freebayes [07:43:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:43:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:43:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:43:35] Found vcfuniq - /usr/local/bin/vcfuniq [07:43:35] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:43:35] Found gzip - /bin/gzip [07:43:35] Found vt - /usr/local/bin/vt [07:43:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:43:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:43:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:43:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:43:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:43:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:43:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:43:36] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:43:54] This is snippy 4.6.0
Show full stderr[07:43:54] This is snippy 4.6.0 [07:43:54] Written by Torsten Seemann [07:43:54] Obtained from https://github.com/tseemann/snippy [07:43:54] Detected operating system: linux [07:43:54] Enabling bundled linux tools. [07:43:54] Found bwa - /usr/local/bin/bwa [07:43:54] Found bcftools - /usr/local/bin/bcftools [07:43:54] Found samtools - /usr/local/bin/samtools [07:43:54] Found java - /usr/local/bin/java [07:43:54] Found snpEff - /usr/local/bin/snpEff [07:43:54] Found samclip - /usr/local/bin/samclip [07:43:54] Found seqtk - /usr/local/bin/seqtk [07:43:54] Found parallel - /usr/local/bin/parallel [07:43:54] Found freebayes - /usr/local/bin/freebayes [07:43:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:43:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:43:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:43:54] Found vcfuniq - /usr/local/bin/vcfuniq [07:43:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:43:54] Found gzip - /bin/gzip [07:43:54] Found vt - /usr/local/bin/vt [07:43:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:43:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:43:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:43:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:43:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:43:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:43:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:43:55] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:45:01] This is snippy 4.6.0
Show full stderr[07:45:01] This is snippy 4.6.0 [07:45:01] Written by Torsten Seemann [07:45:01] Obtained from https://github.com/tseemann/snippy [07:45:01] Detected operating system: linux [07:45:01] Enabling bundled linux tools. [07:45:01] Found bwa - /usr/local/bin/bwa [07:45:01] Found bcftools - /usr/local/bin/bcftools [07:45:01] Found samtools - /usr/local/bin/samtools [07:45:01] Found java - /usr/local/bin/java [07:45:01] Found snpEff - /usr/local/bin/snpEff [07:45:01] Found samclip - /usr/local/bin/samclip [07:45:01] Found seqtk - /usr/local/bin/seqtk [07:45:01] Found parallel - /usr/local/bin/parallel [07:45:01] Found freebayes - /usr/local/bin/freebayes [07:45:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:45:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:45:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:45:01] Found vcfuniq - /usr/local/bin/vcfuniq [07:45:01] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:45:01] Found gzip - /bin/gzip [07:45:01] Found vt - /usr/local/bin/vt [07:45:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:45:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:45:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:45:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:45:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:45:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:45:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:45:02] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:45:34] This is snippy 4.6.0
Show full stderr[07:45:34] This is snippy 4.6.0 [07:45:34] Written by Torsten Seemann [07:45:34] Obtained from https://github.com/tseemann/snippy [07:45:34] Detected operating system: linux [07:45:34] Enabling bundled linux tools. [07:45:34] Found bwa - /usr/local/bin/bwa [07:45:34] Found bcftools - /usr/local/bin/bcftools [07:45:34] Found samtools - /usr/local/bin/samtools [07:45:34] Found java - /usr/local/bin/java [07:45:34] Found snpEff - /usr/local/bin/snpEff [07:45:34] Found samclip - /usr/local/bin/samclip [07:45:34] Found seqtk - /usr/local/bin/seqtk [07:45:34] Found parallel - /usr/local/bin/parallel [07:45:34] Found freebayes - /usr/local/bin/freebayes [07:45:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:45:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:45:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:45:34] Found vcfuniq - /usr/local/bin/vcfuniq [07:45:34] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:45:34] Found gzip - /bin/gzip [07:45:34] Found vt - /usr/local/bin/vt [07:45:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:45:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:45:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:45:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:45:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:45:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:45:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:45:35] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:46:07] This is snippy 4.6.0
Show full stderr[07:46:07] This is snippy 4.6.0 [07:46:07] Written by Torsten Seemann [07:46:07] Obtained from https://github.com/tseemann/snippy [07:46:07] Detected operating system: linux [07:46:07] Enabling bundled linux tools. [07:46:07] Found bwa - /usr/local/bin/bwa [07:46:07] Found bcftools - /usr/local/bin/bcftools [07:46:07] Found samtools - /usr/local/bin/samtools [07:46:07] Found java - /usr/local/bin/java [07:46:07] Found snpEff - /usr/local/bin/snpEff [07:46:07] Found samclip - /usr/local/bin/samclip [07:46:07] Found seqtk - /usr/local/bin/seqtk [07:46:07] Found parallel - /usr/local/bin/parallel [07:46:07] Found freebayes - /usr/local/bin/freebayes [07:46:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:46:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:46:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:46:07] Found vcfuniq - /usr/local/bin/vcfuniq [07:46:07] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:46:07] Found gzip - /bin/gzip [07:46:07] Found vt - /usr/local/bin/vt [07:46:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:46:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:46:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:46:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:46:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:46:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:46:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:46:08] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:46:36] This is snippy 4.6.0
Show full stderr[07:46:36] This is snippy 4.6.0 [07:46:36] Written by Torsten Seemann [07:46:36] Obtained from https://github.com/tseemann/snippy [07:46:36] Detected operating system: linux [07:46:36] Enabling bundled linux tools. [07:46:37] Found bwa - /usr/local/bin/bwa [07:46:37] Found bcftools - /usr/local/bin/bcftools [07:46:37] Found samtools - /usr/local/bin/samtools [07:46:37] Found java - /usr/local/bin/java [07:46:37] Found snpEff - /usr/local/bin/snpEff [07:46:37] Found samclip - /usr/local/bin/samclip [07:46:37] Found seqtk - /usr/local/bin/seqtk [07:46:37] Found parallel - /usr/local/bin/parallel [07:46:37] Found freebayes - /usr/local/bin/freebayes [07:46:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:46:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:46:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:46:37] Found vcfuniq - /usr/local/bin/vcfuniq [07:46:37] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:46:37] Found gzip - /bin/gzip [07:46:37] Found vt - /usr/local/bin/vt [07:46:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:46:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:46:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:46:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:46:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:46:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:46:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:46:37] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:43:28] This is snippy 4.6.0
Show full stderr[07:43:28] This is snippy 4.6.0 [07:43:28] Written by Torsten Seemann [07:43:28] Obtained from https://github.com/tseemann/snippy [07:43:28] Detected operating system: linux [07:43:28] Enabling bundled linux tools. [07:43:28] Found bwa - /usr/local/bin/bwa [07:43:28] Found bcftools - /usr/local/bin/bcftools [07:43:28] Found samtools - /usr/local/bin/samtools [07:43:28] Found java - /usr/local/bin/java [07:43:28] Found snpEff - /usr/local/bin/snpEff [07:43:28] Found samclip - /usr/local/bin/samclip [07:43:28] Found seqtk - /usr/local/bin/seqtk [07:43:28] Found parallel - /usr/local/bin/parallel [07:43:28] Found freebayes - /usr/local/bin/freebayes [07:43:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:43:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:43:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:43:28] Found vcfuniq - /usr/local/bin/vcfuniq [07:43:28] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:43:28] Found gzip - /bin/gzip [07:43:28] Found vt - /usr/local/bin/vt [07:43:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:43:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:43:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:43:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:43:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:43:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:43:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:43:29] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:43:38] This is snippy 4.6.0
Show full stderr[07:43:38] This is snippy 4.6.0 [07:43:38] Written by Torsten Seemann [07:43:38] Obtained from https://github.com/tseemann/snippy [07:43:38] Detected operating system: linux [07:43:38] Enabling bundled linux tools. [07:43:38] Found bwa - /usr/local/bin/bwa [07:43:38] Found bcftools - /usr/local/bin/bcftools [07:43:38] Found samtools - /usr/local/bin/samtools [07:43:38] Found java - /usr/local/bin/java [07:43:38] Found snpEff - /usr/local/bin/snpEff [07:43:38] Found samclip - /usr/local/bin/samclip [07:43:38] Found seqtk - /usr/local/bin/seqtk [07:43:38] Found parallel - /usr/local/bin/parallel [07:43:38] Found freebayes - /usr/local/bin/freebayes [07:43:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:43:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:43:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:43:38] Found vcfuniq - /usr/local/bin/vcfuniq [07:43:38] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:43:38] Found gzip - /bin/gzip [07:43:38] Found vt - /usr/local/bin/vt [07:43:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:43:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:43:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:43:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:43:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:43:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:43:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:43:39] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:43:41] This is snippy 4.6.0
Show full stderr[07:43:41] This is snippy 4.6.0 [07:43:41] Written by Torsten Seemann [07:43:41] Obtained from https://github.com/tseemann/snippy [07:43:41] Detected operating system: linux [07:43:41] Enabling bundled linux tools. [07:43:41] Found bwa - /usr/local/bin/bwa [07:43:41] Found bcftools - /usr/local/bin/bcftools [07:43:41] Found samtools - /usr/local/bin/samtools [07:43:41] Found java - /usr/local/bin/java [07:43:41] Found snpEff - /usr/local/bin/snpEff [07:43:41] Found samclip - /usr/local/bin/samclip [07:43:41] Found seqtk - /usr/local/bin/seqtk [07:43:41] Found parallel - /usr/local/bin/parallel [07:43:41] Found freebayes - /usr/local/bin/freebayes [07:43:41] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:43:41] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:43:41] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:43:41] Found vcfuniq - /usr/local/bin/vcfuniq [07:43:41] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:43:41] Found gzip - /bin/gzip [07:43:41] Found vt - /usr/local/bin/vt [07:43:41] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:43:41] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:43:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:43:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:43:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:43:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:43:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:43:42] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:44:00] This is snippy 4.6.0
Show full stderr[07:44:00] This is snippy 4.6.0 [07:44:00] Written by Torsten Seemann [07:44:00] Obtained from https://github.com/tseemann/snippy [07:44:00] Detected operating system: linux [07:44:00] Enabling bundled linux tools. [07:44:00] Found bwa - /usr/local/bin/bwa [07:44:00] Found bcftools - /usr/local/bin/bcftools [07:44:00] Found samtools - /usr/local/bin/samtools [07:44:00] Found java - /usr/local/bin/java [07:44:00] Found snpEff - /usr/local/bin/snpEff [07:44:00] Found samclip - /usr/local/bin/samclip [07:44:00] Found seqtk - /usr/local/bin/seqtk [07:44:00] Found parallel - /usr/local/bin/parallel [07:44:00] Found freebayes - /usr/local/bin/freebayes [07:44:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:44:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:44:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:44:00] Found vcfuniq - /usr/local/bin/vcfuniq [07:44:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:44:00] Found gzip - /bin/gzip [07:44:00] Found vt - /usr/local/bin/vt [07:44:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:44:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:44:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:44:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:44:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:44:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:44:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:44:01] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:44:35] This is snippy 4.6.0
Show full stderr[07:44:35] This is snippy 4.6.0 [07:44:35] Written by Torsten Seemann [07:44:35] Obtained from https://github.com/tseemann/snippy [07:44:35] Detected operating system: linux [07:44:35] Enabling bundled linux tools. [07:44:35] Found bwa - /usr/local/bin/bwa [07:44:35] Found bcftools - /usr/local/bin/bcftools [07:44:35] Found samtools - /usr/local/bin/samtools [07:44:35] Found java - /usr/local/bin/java [07:44:35] Found snpEff - /usr/local/bin/snpEff [07:44:35] Found samclip - /usr/local/bin/samclip [07:44:35] Found seqtk - /usr/local/bin/seqtk [07:44:35] Found parallel - /usr/local/bin/parallel [07:44:35] Found freebayes - /usr/local/bin/freebayes [07:44:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:44:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:44:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:44:35] Found vcfuniq - /usr/local/bin/vcfuniq [07:44:35] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:44:35] Found gzip - /bin/gzip [07:44:35] Found vt - /usr/local/bin/vt [07:44:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:44:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:44:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:44:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:44:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:44:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:44:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:44:36] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:44:58] This is snippy 4.6.0
Show full stderr[07:44:58] This is snippy 4.6.0 [07:44:58] Written by Torsten Seemann [07:44:58] Obtained from https://github.com/tseemann/snippy [07:44:58] Detected operating system: linux [07:44:58] Enabling bundled linux tools. [07:44:58] Found bwa - /usr/local/bin/bwa [07:44:58] Found bcftools - /usr/local/bin/bcftools [07:44:58] Found samtools - /usr/local/bin/samtools [07:44:58] Found java - /usr/local/bin/java [07:44:58] Found snpEff - /usr/local/bin/snpEff [07:44:58] Found samclip - /usr/local/bin/samclip [07:44:58] Found seqtk - /usr/local/bin/seqtk [07:44:58] Found parallel - /usr/local/bin/parallel [07:44:58] Found freebayes - /usr/local/bin/freebayes [07:44:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:44:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:44:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:44:58] Found vcfuniq - /usr/local/bin/vcfuniq [07:44:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:44:58] Found gzip - /bin/gzip [07:44:58] Found vt - /usr/local/bin/vt [07:44:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:44:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:44:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:44:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:44:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:44:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:44:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:44:59] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:45:10] This is snippy 4.6.0
Show full stderr[07:45:10] This is snippy 4.6.0 [07:45:10] Written by Torsten Seemann [07:45:10] Obtained from https://github.com/tseemann/snippy [07:45:10] Detected operating system: linux [07:45:10] Enabling bundled linux tools. [07:45:10] Found bwa - /usr/local/bin/bwa [07:45:10] Found bcftools - /usr/local/bin/bcftools [07:45:10] Found samtools - /usr/local/bin/samtools [07:45:10] Found java - /usr/local/bin/java [07:45:10] Found snpEff - /usr/local/bin/snpEff [07:45:10] Found samclip - /usr/local/bin/samclip [07:45:10] Found seqtk - /usr/local/bin/seqtk [07:45:10] Found parallel - /usr/local/bin/parallel [07:45:10] Found freebayes - /usr/local/bin/freebayes [07:45:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:45:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:45:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:45:10] Found vcfuniq - /usr/local/bin/vcfuniq [07:45:10] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:45:10] Found gzip - /bin/gzip [07:45:10] Found vt - /usr/local/bin/vt [07:45:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:45:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:45:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:45:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:45:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:45:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:45:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:45:11] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:45:22] This is snippy 4.6.0
Show full stderr[07:45:22] This is snippy 4.6.0 [07:45:22] Written by Torsten Seemann [07:45:22] Obtained from https://github.com/tseemann/snippy [07:45:22] Detected operating system: linux [07:45:22] Enabling bundled linux tools. [07:45:22] Found bwa - /usr/local/bin/bwa [07:45:22] Found bcftools - /usr/local/bin/bcftools [07:45:22] Found samtools - /usr/local/bin/samtools [07:45:22] Found java - /usr/local/bin/java [07:45:22] Found snpEff - /usr/local/bin/snpEff [07:45:22] Found samclip - /usr/local/bin/samclip [07:45:22] Found seqtk - /usr/local/bin/seqtk [07:45:22] Found parallel - /usr/local/bin/parallel [07:45:22] Found freebayes - /usr/local/bin/freebayes [07:45:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:45:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:45:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:45:22] Found vcfuniq - /usr/local/bin/vcfuniq [07:45:22] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:45:22] Found gzip - /bin/gzip [07:45:22] Found vt - /usr/local/bin/vt [07:45:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:45:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:45:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:45:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:45:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:45:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:45:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:45:23] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:46:22] This is snippy 4.6.0
Show full stderr[07:46:22] This is snippy 4.6.0 [07:46:22] Written by Torsten Seemann [07:46:22] Obtained from https://github.com/tseemann/snippy [07:46:22] Detected operating system: linux [07:46:22] Enabling bundled linux tools. [07:46:22] Found bwa - /usr/local/bin/bwa [07:46:22] Found bcftools - /usr/local/bin/bcftools [07:46:22] Found samtools - /usr/local/bin/samtools [07:46:22] Found java - /usr/local/bin/java [07:46:22] Found snpEff - /usr/local/bin/snpEff [07:46:22] Found samclip - /usr/local/bin/samclip [07:46:22] Found seqtk - /usr/local/bin/seqtk [07:46:22] Found parallel - /usr/local/bin/parallel [07:46:22] Found freebayes - /usr/local/bin/freebayes [07:46:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:46:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:46:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:46:22] Found vcfuniq - /usr/local/bin/vcfuniq [07:46:22] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:46:22] Found gzip - /bin/gzip [07:46:22] Found vt - /usr/local/bin/vt [07:46:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:46:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:46:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:46:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:46:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:46:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:46:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:46:23] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:38:28] This is snippy 4.6.0
Show full stderr[07:38:28] This is snippy 4.6.0 [07:38:28] Written by Torsten Seemann [07:38:28] Obtained from https://github.com/tseemann/snippy [07:38:28] Detected operating system: linux [07:38:28] Enabling bundled linux tools. [07:38:28] Found bwa - /usr/local/bin/bwa [07:38:28] Found bcftools - /usr/local/bin/bcftools [07:38:28] Found samtools - /usr/local/bin/samtools [07:38:28] Found java - /usr/local/bin/java [07:38:28] Found snpEff - /usr/local/bin/snpEff [07:38:28] Found samclip - /usr/local/bin/samclip [07:38:28] Found seqtk - /usr/local/bin/seqtk [07:38:28] Found parallel - /usr/local/bin/parallel [07:38:28] Found freebayes - /usr/local/bin/freebayes [07:38:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:38:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:38:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:38:28] Found vcfuniq - /usr/local/bin/vcfuniq [07:38:28] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:38:28] Found gzip - /bin/gzip [07:38:28] Found vt - /usr/local/bin/vt [07:38:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:38:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:38:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:38:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:38:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:38:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:38:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:38:29] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:40:24] This is snippy 4.6.0
Show full stderr[07:40:24] This is snippy 4.6.0 [07:40:24] Written by Torsten Seemann [07:40:24] Obtained from https://github.com/tseemann/snippy [07:40:24] Detected operating system: linux [07:40:24] Enabling bundled linux tools. [07:40:24] Found bwa - /usr/local/bin/bwa [07:40:24] Found bcftools - /usr/local/bin/bcftools [07:40:24] Found samtools - /usr/local/bin/samtools [07:40:24] Found java - /usr/local/bin/java [07:40:24] Found snpEff - /usr/local/bin/snpEff [07:40:25] Found samclip - /usr/local/bin/samclip [07:40:25] Found seqtk - /usr/local/bin/seqtk [07:40:25] Found parallel - /usr/local/bin/parallel [07:40:25] Found freebayes - /usr/local/bin/freebayes [07:40:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:40:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:40:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:40:25] Found vcfuniq - /usr/local/bin/vcfuniq [07:40:25] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:40:25] Found gzip - /bin/gzip [07:40:25] Found vt - /usr/local/bin/vt [07:40:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:40:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:40:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:40:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:40:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:40:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:40:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:40:25] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:40:50] This is snippy 4.6.0
Show full stderr[07:40:50] This is snippy 4.6.0 [07:40:50] Written by Torsten Seemann [07:40:50] Obtained from https://github.com/tseemann/snippy [07:40:50] Detected operating system: linux [07:40:50] Enabling bundled linux tools. [07:40:51] Found bwa - /usr/local/bin/bwa [07:40:51] Found bcftools - /usr/local/bin/bcftools [07:40:51] Found samtools - /usr/local/bin/samtools [07:40:51] Found java - /usr/local/bin/java [07:40:51] Found snpEff - /usr/local/bin/snpEff [07:40:51] Found samclip - /usr/local/bin/samclip [07:40:51] Found seqtk - /usr/local/bin/seqtk [07:40:51] Found parallel - /usr/local/bin/parallel [07:40:51] Found freebayes - /usr/local/bin/freebayes [07:40:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:40:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:40:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:40:51] Found vcfuniq - /usr/local/bin/vcfuniq [07:40:51] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:40:51] Found gzip - /bin/gzip [07:40:51] Found vt - /usr/local/bin/vt [07:40:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:40:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:40:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:40:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:40:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:40:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:40:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:40:51] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:41:13] This is snippy 4.6.0
Show full stderr[07:41:13] This is snippy 4.6.0 [07:41:13] Written by Torsten Seemann [07:41:13] Obtained from https://github.com/tseemann/snippy [07:41:13] Detected operating system: linux [07:41:13] Enabling bundled linux tools. [07:41:13] Found bwa - /usr/local/bin/bwa [07:41:13] Found bcftools - /usr/local/bin/bcftools [07:41:13] Found samtools - /usr/local/bin/samtools [07:41:13] Found java - /usr/local/bin/java [07:41:13] Found snpEff - /usr/local/bin/snpEff [07:41:13] Found samclip - /usr/local/bin/samclip [07:41:13] Found seqtk - /usr/local/bin/seqtk [07:41:13] Found parallel - /usr/local/bin/parallel [07:41:13] Found freebayes - /usr/local/bin/freebayes [07:41:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:41:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:41:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:41:13] Found vcfuniq - /usr/local/bin/vcfuniq [07:41:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:41:13] Found gzip - /bin/gzip [07:41:13] Found vt - /usr/local/bin/vt [07:41:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:41:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:41:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:41:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:41:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:41:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:41:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:41:13] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:41:16] This is snippy 4.6.0
Show full stderr[07:41:16] This is snippy 4.6.0 [07:41:16] Written by Torsten Seemann [07:41:16] Obtained from https://github.com/tseemann/snippy [07:41:16] Detected operating system: linux [07:41:16] Enabling bundled linux tools. [07:41:16] Found bwa - /usr/local/bin/bwa [07:41:16] Found bcftools - /usr/local/bin/bcftools [07:41:16] Found samtools - /usr/local/bin/samtools [07:41:16] Found java - /usr/local/bin/java [07:41:16] Found snpEff - /usr/local/bin/snpEff [07:41:16] Found samclip - /usr/local/bin/samclip [07:41:16] Found seqtk - /usr/local/bin/seqtk [07:41:16] Found parallel - /usr/local/bin/parallel [07:41:16] Found freebayes - /usr/local/bin/freebayes [07:41:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:41:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:41:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:41:16] Found vcfuniq - /usr/local/bin/vcfuniq [07:41:16] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:41:16] Found gzip - /bin/gzip [07:41:16] Found vt - /usr/local/bin/vt [07:41:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:41:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:41:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:41:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:41:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:41:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:41:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:41:16] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:41:40] This is snippy 4.6.0
Show full stderr[07:41:40] This is snippy 4.6.0 [07:41:40] Written by Torsten Seemann [07:41:40] Obtained from https://github.com/tseemann/snippy [07:41:40] Detected operating system: linux [07:41:40] Enabling bundled linux tools. [07:41:40] Found bwa - /usr/local/bin/bwa [07:41:40] Found bcftools - /usr/local/bin/bcftools [07:41:40] Found samtools - /usr/local/bin/samtools [07:41:40] Found java - /usr/local/bin/java [07:41:40] Found snpEff - /usr/local/bin/snpEff [07:41:40] Found samclip - /usr/local/bin/samclip [07:41:40] Found seqtk - /usr/local/bin/seqtk [07:41:40] Found parallel - /usr/local/bin/parallel [07:41:40] Found freebayes - /usr/local/bin/freebayes [07:41:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:41:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:41:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:41:40] Found vcfuniq - /usr/local/bin/vcfuniq [07:41:40] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:41:40] Found gzip - /bin/gzip [07:41:40] Found vt - /usr/local/bin/vt [07:41:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:41:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:41:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:41:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:41:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:41:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:41:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:41:41] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:41:42] This is snippy 4.6.0
Show full stderr[07:41:42] This is snippy 4.6.0 [07:41:42] Written by Torsten Seemann [07:41:42] Obtained from https://github.com/tseemann/snippy [07:41:42] Detected operating system: linux [07:41:42] Enabling bundled linux tools. [07:41:42] Found bwa - /usr/local/bin/bwa [07:41:42] Found bcftools - /usr/local/bin/bcftools [07:41:42] Found samtools - /usr/local/bin/samtools [07:41:42] Found java - /usr/local/bin/java [07:41:43] Found snpEff - /usr/local/bin/snpEff [07:41:43] Found samclip - /usr/local/bin/samclip [07:41:43] Found seqtk - /usr/local/bin/seqtk [07:41:43] Found parallel - /usr/local/bin/parallel [07:41:43] Found freebayes - /usr/local/bin/freebayes [07:41:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:41:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:41:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:41:43] Found vcfuniq - /usr/local/bin/vcfuniq [07:41:43] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:41:43] Found gzip - /bin/gzip [07:41:43] Found vt - /usr/local/bin/vt [07:41:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:41:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:41:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:41:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:41:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:41:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:41:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:41:43] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:47:34] This is snippy 4.6.0
Show full stderr[07:47:34] This is snippy 4.6.0 [07:47:34] Written by Torsten Seemann [07:47:34] Obtained from https://github.com/tseemann/snippy [07:47:34] Detected operating system: linux [07:47:34] Enabling bundled linux tools. [07:47:34] Found bwa - /usr/local/bin/bwa [07:47:34] Found bcftools - /usr/local/bin/bcftools [07:47:34] Found samtools - /usr/local/bin/samtools [07:47:34] Found java - /usr/local/bin/java [07:47:34] Found snpEff - /usr/local/bin/snpEff [07:47:34] Found samclip - /usr/local/bin/samclip [07:47:34] Found seqtk - /usr/local/bin/seqtk [07:47:34] Found parallel - /usr/local/bin/parallel [07:47:34] Found freebayes - /usr/local/bin/freebayes [07:47:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:47:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:47:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:47:34] Found vcfuniq - /usr/local/bin/vcfuniq [07:47:34] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:47:34] Found gzip - /bin/gzip [07:47:34] Found vt - /usr/local/bin/vt [07:47:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:47:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:47:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:47:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:47:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:47:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:47:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:47:35] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:47:44] This is snippy 4.6.0
Show full stderr[07:47:44] This is snippy 4.6.0 [07:47:44] Written by Torsten Seemann [07:47:44] Obtained from https://github.com/tseemann/snippy [07:47:44] Detected operating system: linux [07:47:44] Enabling bundled linux tools. [07:47:44] Found bwa - /usr/local/bin/bwa [07:47:44] Found bcftools - /usr/local/bin/bcftools [07:47:44] Found samtools - /usr/local/bin/samtools [07:47:44] Found java - /usr/local/bin/java [07:47:44] Found snpEff - /usr/local/bin/snpEff [07:47:44] Found samclip - /usr/local/bin/samclip [07:47:44] Found seqtk - /usr/local/bin/seqtk [07:47:44] Found parallel - /usr/local/bin/parallel [07:47:44] Found freebayes - /usr/local/bin/freebayes [07:47:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:47:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:47:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:47:44] Found vcfuniq - /usr/local/bin/vcfuniq [07:47:44] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:47:44] Found gzip - /bin/gzip [07:47:44] Found vt - /usr/local/bin/vt [07:47:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:47:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:47:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:47:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:47:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:47:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:47:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:47:45] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:47:47] This is snippy 4.6.0
Show full stderr[07:47:47] This is snippy 4.6.0 [07:47:47] Written by Torsten Seemann [07:47:47] Obtained from https://github.com/tseemann/snippy [07:47:47] Detected operating system: linux [07:47:47] Enabling bundled linux tools. [07:47:47] Found bwa - /usr/local/bin/bwa [07:47:47] Found bcftools - /usr/local/bin/bcftools [07:47:47] Found samtools - /usr/local/bin/samtools [07:47:47] Found java - /usr/local/bin/java [07:47:47] Found snpEff - /usr/local/bin/snpEff [07:47:47] Found samclip - /usr/local/bin/samclip [07:47:47] Found seqtk - /usr/local/bin/seqtk [07:47:47] Found parallel - /usr/local/bin/parallel [07:47:47] Found freebayes - /usr/local/bin/freebayes [07:47:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:47:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:47:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:47:47] Found vcfuniq - /usr/local/bin/vcfuniq [07:47:47] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:47:47] Found gzip - /bin/gzip [07:47:47] Found vt - /usr/local/bin/vt [07:47:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:47:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:47:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:47:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:47:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:47:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:47:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:47:48] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:48:20] This is snippy 4.6.0
Show full stderr[07:48:20] This is snippy 4.6.0 [07:48:20] Written by Torsten Seemann [07:48:20] Obtained from https://github.com/tseemann/snippy [07:48:20] Detected operating system: linux [07:48:20] Enabling bundled linux tools. [07:48:20] Found bwa - /usr/local/bin/bwa [07:48:20] Found bcftools - /usr/local/bin/bcftools [07:48:20] Found samtools - /usr/local/bin/samtools [07:48:20] Found java - /usr/local/bin/java [07:48:20] Found snpEff - /usr/local/bin/snpEff [07:48:20] Found samclip - /usr/local/bin/samclip [07:48:20] Found seqtk - /usr/local/bin/seqtk [07:48:20] Found parallel - /usr/local/bin/parallel [07:48:20] Found freebayes - /usr/local/bin/freebayes [07:48:20] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:48:20] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:48:20] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:48:20] Found vcfuniq - /usr/local/bin/vcfuniq [07:48:20] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:48:20] Found gzip - /bin/gzip [07:48:20] Found vt - /usr/local/bin/vt [07:48:20] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:48:20] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:48:20] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:48:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:48:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:48:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:48:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:48:21] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:48:23] This is snippy 4.6.0
Show full stderr[07:48:23] This is snippy 4.6.0 [07:48:23] Written by Torsten Seemann [07:48:23] Obtained from https://github.com/tseemann/snippy [07:48:23] Detected operating system: linux [07:48:23] Enabling bundled linux tools. [07:48:23] Found bwa - /usr/local/bin/bwa [07:48:23] Found bcftools - /usr/local/bin/bcftools [07:48:23] Found samtools - /usr/local/bin/samtools [07:48:23] Found java - /usr/local/bin/java [07:48:23] Found snpEff - /usr/local/bin/snpEff [07:48:23] Found samclip - /usr/local/bin/samclip [07:48:23] Found seqtk - /usr/local/bin/seqtk [07:48:23] Found parallel - /usr/local/bin/parallel [07:48:23] Found freebayes - /usr/local/bin/freebayes [07:48:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:48:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:48:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:48:23] Found vcfuniq - /usr/local/bin/vcfuniq [07:48:23] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:48:23] Found gzip - /bin/gzip [07:48:23] Found vt - /usr/local/bin/vt [07:48:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:48:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:48:23] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:48:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:48:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:48:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:48:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:48:24] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:48:29] This is snippy 4.6.0
Show full stderr[07:48:29] This is snippy 4.6.0 [07:48:29] Written by Torsten Seemann [07:48:29] Obtained from https://github.com/tseemann/snippy [07:48:29] Detected operating system: linux [07:48:29] Enabling bundled linux tools. [07:48:29] Found bwa - /usr/local/bin/bwa [07:48:29] Found bcftools - /usr/local/bin/bcftools [07:48:29] Found samtools - /usr/local/bin/samtools [07:48:29] Found java - /usr/local/bin/java [07:48:29] Found snpEff - /usr/local/bin/snpEff [07:48:29] Found samclip - /usr/local/bin/samclip [07:48:29] Found seqtk - /usr/local/bin/seqtk [07:48:29] Found parallel - /usr/local/bin/parallel [07:48:29] Found freebayes - /usr/local/bin/freebayes [07:48:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:48:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:48:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:48:29] Found vcfuniq - /usr/local/bin/vcfuniq [07:48:29] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:48:29] Found gzip - /bin/gzip [07:48:29] Found vt - /usr/local/bin/vt [07:48:29] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:48:29] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:48:29] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:48:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:48:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:48:30] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:48:30] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:48:30] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:48:32] This is snippy 4.6.0
Show full stderr[07:48:32] This is snippy 4.6.0 [07:48:32] Written by Torsten Seemann [07:48:32] Obtained from https://github.com/tseemann/snippy [07:48:32] Detected operating system: linux [07:48:32] Enabling bundled linux tools. [07:48:32] Found bwa - /usr/local/bin/bwa [07:48:32] Found bcftools - /usr/local/bin/bcftools [07:48:32] Found samtools - /usr/local/bin/samtools [07:48:32] Found java - /usr/local/bin/java [07:48:32] Found snpEff - /usr/local/bin/snpEff [07:48:32] Found samclip - /usr/local/bin/samclip [07:48:32] Found seqtk - /usr/local/bin/seqtk [07:48:32] Found parallel - /usr/local/bin/parallel [07:48:32] Found freebayes - /usr/local/bin/freebayes [07:48:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:48:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:48:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:48:32] Found vcfuniq - /usr/local/bin/vcfuniq [07:48:32] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:48:32] Found gzip - /bin/gzip [07:48:32] Found vt - /usr/local/bin/vt [07:48:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:48:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:48:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:48:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:48:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:48:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:48:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:48:33] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:48:34] This is snippy 4.6.0
Show full stderr[07:48:34] This is snippy 4.6.0 [07:48:34] Written by Torsten Seemann [07:48:34] Obtained from https://github.com/tseemann/snippy [07:48:34] Detected operating system: linux [07:48:34] Enabling bundled linux tools. [07:48:34] Found bwa - /usr/local/bin/bwa [07:48:34] Found bcftools - /usr/local/bin/bcftools [07:48:34] Found samtools - /usr/local/bin/samtools [07:48:34] Found java - /usr/local/bin/java [07:48:34] Found snpEff - /usr/local/bin/snpEff [07:48:34] Found samclip - /usr/local/bin/samclip [07:48:34] Found seqtk - /usr/local/bin/seqtk [07:48:34] Found parallel - /usr/local/bin/parallel [07:48:34] Found freebayes - /usr/local/bin/freebayes [07:48:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:48:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:48:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:48:34] Found vcfuniq - /usr/local/bin/vcfuniq [07:48:34] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:48:34] Found gzip - /bin/gzip [07:48:34] Found vt - /usr/local/bin/vt [07:48:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:48:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:48:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:48:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:48:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:48:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:48:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:48:35] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:48:38] This is snippy 4.6.0
Show full stderr[07:48:38] This is snippy 4.6.0 [07:48:38] Written by Torsten Seemann [07:48:38] Obtained from https://github.com/tseemann/snippy [07:48:38] Detected operating system: linux [07:48:38] Enabling bundled linux tools. [07:48:38] Found bwa - /usr/local/bin/bwa [07:48:38] Found bcftools - /usr/local/bin/bcftools [07:48:38] Found samtools - /usr/local/bin/samtools [07:48:38] Found java - /usr/local/bin/java [07:48:38] Found snpEff - /usr/local/bin/snpEff [07:48:38] Found samclip - /usr/local/bin/samclip [07:48:38] Found seqtk - /usr/local/bin/seqtk [07:48:38] Found parallel - /usr/local/bin/parallel [07:48:38] Found freebayes - /usr/local/bin/freebayes [07:48:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:48:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:48:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:48:38] Found vcfuniq - /usr/local/bin/vcfuniq [07:48:38] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:48:38] Found gzip - /bin/gzip [07:48:38] Found vt - /usr/local/bin/vt [07:48:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:48:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:48:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:48:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:48:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:48:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:48:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:48:39] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:48:44] This is snippy 4.6.0
Show full stderr[07:48:44] This is snippy 4.6.0 [07:48:44] Written by Torsten Seemann [07:48:44] Obtained from https://github.com/tseemann/snippy [07:48:44] Detected operating system: linux [07:48:44] Enabling bundled linux tools. [07:48:44] Found bwa - /usr/local/bin/bwa [07:48:44] Found bcftools - /usr/local/bin/bcftools [07:48:44] Found samtools - /usr/local/bin/samtools [07:48:44] Found java - /usr/local/bin/java [07:48:44] Found snpEff - /usr/local/bin/snpEff [07:48:44] Found samclip - /usr/local/bin/samclip [07:48:44] Found seqtk - /usr/local/bin/seqtk [07:48:44] Found parallel - /usr/local/bin/parallel [07:48:44] Found freebayes - /usr/local/bin/freebayes [07:48:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:48:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:48:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:48:44] Found vcfuniq - /usr/local/bin/vcfuniq [07:48:44] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:48:44] Found gzip - /bin/gzip [07:48:44] Found vt - /usr/local/bin/vt [07:48:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:48:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:48:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:48:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:48:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:48:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:48:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:48:45] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:42:07] This is snippy 4.6.0
Show full stderr[07:42:07] This is snippy 4.6.0 [07:42:07] Written by Torsten Seemann [07:42:07] Obtained from https://github.com/tseemann/snippy [07:42:07] Detected operating system: linux [07:42:07] Enabling bundled linux tools. [07:42:07] Found bwa - /usr/local/bin/bwa [07:42:07] Found bcftools - /usr/local/bin/bcftools [07:42:07] Found samtools - /usr/local/bin/samtools [07:42:07] Found java - /usr/local/bin/java [07:42:07] Found snpEff - /usr/local/bin/snpEff [07:42:07] Found samclip - /usr/local/bin/samclip [07:42:07] Found seqtk - /usr/local/bin/seqtk [07:42:07] Found parallel - /usr/local/bin/parallel [07:42:07] Found freebayes - /usr/local/bin/freebayes [07:42:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:42:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:42:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:42:07] Found vcfuniq - /usr/local/bin/vcfuniq [07:42:07] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:42:07] Found gzip - /bin/gzip [07:42:07] Found vt - /usr/local/bin/vt [07:42:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:42:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:42:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:42:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:42:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:42:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:42:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:42:08] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:42:25] This is snippy 4.6.0
Show full stderr[07:42:25] This is snippy 4.6.0 [07:42:25] Written by Torsten Seemann [07:42:25] Obtained from https://github.com/tseemann/snippy [07:42:25] Detected operating system: linux [07:42:25] Enabling bundled linux tools. [07:42:25] Found bwa - /usr/local/bin/bwa [07:42:25] Found bcftools - /usr/local/bin/bcftools [07:42:25] Found samtools - /usr/local/bin/samtools [07:42:25] Found java - /usr/local/bin/java [07:42:25] Found snpEff - /usr/local/bin/snpEff [07:42:25] Found samclip - /usr/local/bin/samclip [07:42:25] Found seqtk - /usr/local/bin/seqtk [07:42:25] Found parallel - /usr/local/bin/parallel [07:42:25] Found freebayes - /usr/local/bin/freebayes [07:42:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:42:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:42:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:42:25] Found vcfuniq - /usr/local/bin/vcfuniq [07:42:25] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:42:25] Found gzip - /bin/gzip [07:42:25] Found vt - /usr/local/bin/vt [07:42:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:42:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:42:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:42:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:42:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:42:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:42:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:42:25] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:42:46] This is snippy 4.6.0
Show full stderr[07:42:46] This is snippy 4.6.0 [07:42:46] Written by Torsten Seemann [07:42:46] Obtained from https://github.com/tseemann/snippy [07:42:46] Detected operating system: linux [07:42:46] Enabling bundled linux tools. [07:42:46] Found bwa - /usr/local/bin/bwa [07:42:46] Found bcftools - /usr/local/bin/bcftools [07:42:46] Found samtools - /usr/local/bin/samtools [07:42:46] Found java - /usr/local/bin/java [07:42:46] Found snpEff - /usr/local/bin/snpEff [07:42:46] Found samclip - /usr/local/bin/samclip [07:42:46] Found seqtk - /usr/local/bin/seqtk [07:42:46] Found parallel - /usr/local/bin/parallel [07:42:46] Found freebayes - /usr/local/bin/freebayes [07:42:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:42:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:42:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:42:46] Found vcfuniq - /usr/local/bin/vcfuniq [07:42:46] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:42:46] Found gzip - /bin/gzip [07:42:46] Found vt - /usr/local/bin/vt [07:42:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:42:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:42:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:42:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:42:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:42:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:42:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:42:47] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:43:07] This is snippy 4.6.0
Show full stderr[07:43:07] This is snippy 4.6.0 [07:43:07] Written by Torsten Seemann [07:43:07] Obtained from https://github.com/tseemann/snippy [07:43:07] Detected operating system: linux [07:43:07] Enabling bundled linux tools. [07:43:07] Found bwa - /usr/local/bin/bwa [07:43:07] Found bcftools - /usr/local/bin/bcftools [07:43:07] Found samtools - /usr/local/bin/samtools [07:43:07] Found java - /usr/local/bin/java [07:43:07] Found snpEff - /usr/local/bin/snpEff [07:43:07] Found samclip - /usr/local/bin/samclip [07:43:07] Found seqtk - /usr/local/bin/seqtk [07:43:07] Found parallel - /usr/local/bin/parallel [07:43:07] Found freebayes - /usr/local/bin/freebayes [07:43:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:43:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:43:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:43:07] Found vcfuniq - /usr/local/bin/vcfuniq [07:43:07] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:43:07] Found gzip - /bin/gzip [07:43:07] Found vt - /usr/local/bin/vt [07:43:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:43:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:43:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:43:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:43:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:43:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:43:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:43:08] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:44:22] This is snippy 4.6.0
Show full stderr[07:44:22] This is snippy 4.6.0 [07:44:22] Written by Torsten Seemann [07:44:22] Obtained from https://github.com/tseemann/snippy [07:44:22] Detected operating system: linux [07:44:22] Enabling bundled linux tools. [07:44:22] Found bwa - /usr/local/bin/bwa [07:44:22] Found bcftools - /usr/local/bin/bcftools [07:44:22] Found samtools - /usr/local/bin/samtools [07:44:22] Found java - /usr/local/bin/java [07:44:22] Found snpEff - /usr/local/bin/snpEff [07:44:22] Found samclip - /usr/local/bin/samclip [07:44:22] Found seqtk - /usr/local/bin/seqtk [07:44:22] Found parallel - /usr/local/bin/parallel [07:44:22] Found freebayes - /usr/local/bin/freebayes [07:44:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:44:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:44:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:44:22] Found vcfuniq - /usr/local/bin/vcfuniq [07:44:22] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:44:22] Found gzip - /bin/gzip [07:44:22] Found vt - /usr/local/bin/vt [07:44:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:44:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:44:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:44:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:44:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:44:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:44:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:44:23] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:44:46] This is snippy 4.6.0
Show full stderr[07:44:46] This is snippy 4.6.0 [07:44:46] Written by Torsten Seemann [07:44:46] Obtained from https://github.com/tseemann/snippy [07:44:46] Detected operating system: linux [07:44:46] Enabling bundled linux tools. [07:44:46] Found bwa - /usr/local/bin/bwa [07:44:46] Found bcftools - /usr/local/bin/bcftools [07:44:46] Found samtools - /usr/local/bin/samtools [07:44:46] Found java - /usr/local/bin/java [07:44:46] Found snpEff - /usr/local/bin/snpEff [07:44:46] Found samclip - /usr/local/bin/samclip [07:44:46] Found seqtk - /usr/local/bin/seqtk [07:44:46] Found parallel - /usr/local/bin/parallel [07:44:46] Found freebayes - /usr/local/bin/freebayes [07:44:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:44:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:44:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:44:46] Found vcfuniq - /usr/local/bin/vcfuniq [07:44:46] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:44:46] Found gzip - /bin/gzip [07:44:46] Found vt - /usr/local/bin/vt [07:44:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:44:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:44:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:44:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:44:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:44:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:44:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:44:47] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:44:49] This is snippy 4.6.0
Show full stderr[07:44:49] This is snippy 4.6.0 [07:44:49] Written by Torsten Seemann [07:44:49] Obtained from https://github.com/tseemann/snippy [07:44:49] Detected operating system: linux [07:44:49] Enabling bundled linux tools. [07:44:49] Found bwa - /usr/local/bin/bwa [07:44:49] Found bcftools - /usr/local/bin/bcftools [07:44:49] Found samtools - /usr/local/bin/samtools [07:44:49] Found java - /usr/local/bin/java [07:44:49] Found snpEff - /usr/local/bin/snpEff [07:44:49] Found samclip - /usr/local/bin/samclip [07:44:49] Found seqtk - /usr/local/bin/seqtk [07:44:49] Found parallel - /usr/local/bin/parallel [07:44:49] Found freebayes - /usr/local/bin/freebayes [07:44:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:44:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:44:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:44:49] Found vcfuniq - /usr/local/bin/vcfuniq [07:44:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:44:49] Found gzip - /bin/gzip [07:44:49] Found vt - /usr/local/bin/vt [07:44:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:44:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:44:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:44:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:44:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:44:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:44:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:44:50] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:44:55] This is snippy 4.6.0
Show full stderr[07:44:55] This is snippy 4.6.0 [07:44:55] Written by Torsten Seemann [07:44:55] Obtained from https://github.com/tseemann/snippy [07:44:55] Detected operating system: linux [07:44:55] Enabling bundled linux tools. [07:44:55] Found bwa - /usr/local/bin/bwa [07:44:55] Found bcftools - /usr/local/bin/bcftools [07:44:55] Found samtools - /usr/local/bin/samtools [07:44:55] Found java - /usr/local/bin/java [07:44:55] Found snpEff - /usr/local/bin/snpEff [07:44:55] Found samclip - /usr/local/bin/samclip [07:44:55] Found seqtk - /usr/local/bin/seqtk [07:44:55] Found parallel - /usr/local/bin/parallel [07:44:55] Found freebayes - /usr/local/bin/freebayes [07:44:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:44:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:44:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:44:55] Found vcfuniq - /usr/local/bin/vcfuniq [07:44:55] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:44:55] Found gzip - /bin/gzip [07:44:55] Found vt - /usr/local/bin/vt [07:44:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:44:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:44:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:44:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:44:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:44:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:44:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:44:56] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:45:04] This is snippy 4.6.0
Show full stderr[07:45:04] This is snippy 4.6.0 [07:45:04] Written by Torsten Seemann [07:45:04] Obtained from https://github.com/tseemann/snippy [07:45:04] Detected operating system: linux [07:45:04] Enabling bundled linux tools. [07:45:04] Found bwa - /usr/local/bin/bwa [07:45:04] Found bcftools - /usr/local/bin/bcftools [07:45:04] Found samtools - /usr/local/bin/samtools [07:45:04] Found java - /usr/local/bin/java [07:45:04] Found snpEff - /usr/local/bin/snpEff [07:45:04] Found samclip - /usr/local/bin/samclip [07:45:04] Found seqtk - /usr/local/bin/seqtk [07:45:04] Found parallel - /usr/local/bin/parallel [07:45:04] Found freebayes - /usr/local/bin/freebayes [07:45:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:45:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:45:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:45:04] Found vcfuniq - /usr/local/bin/vcfuniq [07:45:04] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:45:04] Found gzip - /bin/gzip [07:45:04] Found vt - /usr/local/bin/vt [07:45:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:45:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:45:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:45:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:45:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:45:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:45:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:45:05] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:45:16] This is snippy 4.6.0
Show full stderr[07:45:16] This is snippy 4.6.0 [07:45:16] Written by Torsten Seemann [07:45:16] Obtained from https://github.com/tseemann/snippy [07:45:16] Detected operating system: linux [07:45:16] Enabling bundled linux tools. [07:45:16] Found bwa - /usr/local/bin/bwa [07:45:16] Found bcftools - /usr/local/bin/bcftools [07:45:16] Found samtools - /usr/local/bin/samtools [07:45:16] Found java - /usr/local/bin/java [07:45:16] Found snpEff - /usr/local/bin/snpEff [07:45:16] Found samclip - /usr/local/bin/samclip [07:45:16] Found seqtk - /usr/local/bin/seqtk [07:45:16] Found parallel - /usr/local/bin/parallel [07:45:16] Found freebayes - /usr/local/bin/freebayes [07:45:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:45:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:45:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:45:16] Found vcfuniq - /usr/local/bin/vcfuniq [07:45:16] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:45:16] Found gzip - /bin/gzip [07:45:16] Found vt - /usr/local/bin/vt [07:45:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:45:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:45:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:45:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:45:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:45:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:45:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:45:17] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:47:04] This is snippy 4.6.0
Show full stderr[07:47:04] This is snippy 4.6.0 [07:47:04] Written by Torsten Seemann [07:47:04] Obtained from https://github.com/tseemann/snippy [07:47:04] Detected operating system: linux [07:47:04] Enabling bundled linux tools. [07:47:04] Found bwa - /usr/local/bin/bwa [07:47:04] Found bcftools - /usr/local/bin/bcftools [07:47:04] Found samtools - /usr/local/bin/samtools [07:47:04] Found java - /usr/local/bin/java [07:47:04] Found snpEff - /usr/local/bin/snpEff [07:47:04] Found samclip - /usr/local/bin/samclip [07:47:04] Found seqtk - /usr/local/bin/seqtk [07:47:04] Found parallel - /usr/local/bin/parallel [07:47:04] Found freebayes - /usr/local/bin/freebayes [07:47:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:47:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:47:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:47:04] Found vcfuniq - /usr/local/bin/vcfuniq [07:47:04] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:47:04] Found gzip - /bin/gzip [07:47:04] Found vt - /usr/local/bin/vt [07:47:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:47:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:47:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:47:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:47:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:47:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:47:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:47:05] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:47:19] This is snippy 4.6.0
Show full stderr[07:47:19] This is snippy 4.6.0 [07:47:19] Written by Torsten Seemann [07:47:19] Obtained from https://github.com/tseemann/snippy [07:47:19] Detected operating system: linux [07:47:19] Enabling bundled linux tools. [07:47:19] Found bwa - /usr/local/bin/bwa [07:47:19] Found bcftools - /usr/local/bin/bcftools [07:47:19] Found samtools - /usr/local/bin/samtools [07:47:19] Found java - /usr/local/bin/java [07:47:19] Found snpEff - /usr/local/bin/snpEff [07:47:19] Found samclip - /usr/local/bin/samclip [07:47:19] Found seqtk - /usr/local/bin/seqtk [07:47:19] Found parallel - /usr/local/bin/parallel [07:47:19] Found freebayes - /usr/local/bin/freebayes [07:47:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:47:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:47:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:47:19] Found vcfuniq - /usr/local/bin/vcfuniq [07:47:19] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:47:19] Found gzip - /bin/gzip [07:47:19] Found vt - /usr/local/bin/vt [07:47:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:47:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:47:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:47:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:47:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:47:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:47:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:47:20] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:47:59] This is snippy 4.6.0
Show full stderr[07:47:59] This is snippy 4.6.0 [07:47:59] Written by Torsten Seemann [07:47:59] Obtained from https://github.com/tseemann/snippy [07:47:59] Detected operating system: linux [07:47:59] Enabling bundled linux tools. [07:47:59] Found bwa - /usr/local/bin/bwa [07:47:59] Found bcftools - /usr/local/bin/bcftools [07:47:59] Found samtools - /usr/local/bin/samtools [07:47:59] Found java - /usr/local/bin/java [07:47:59] Found snpEff - /usr/local/bin/snpEff [07:47:59] Found samclip - /usr/local/bin/samclip [07:47:59] Found seqtk - /usr/local/bin/seqtk [07:47:59] Found parallel - /usr/local/bin/parallel [07:47:59] Found freebayes - /usr/local/bin/freebayes [07:47:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:47:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:47:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:47:59] Found vcfuniq - /usr/local/bin/vcfuniq [07:47:59] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:47:59] Found gzip - /bin/gzip [07:47:59] Found vt - /usr/local/bin/vt [07:47:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:47:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:47:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:47:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:47:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:48:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:48:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:48:00] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:48:02] This is snippy 4.6.0
Show full stderr[07:48:02] This is snippy 4.6.0 [07:48:02] Written by Torsten Seemann [07:48:02] Obtained from https://github.com/tseemann/snippy [07:48:02] Detected operating system: linux [07:48:02] Enabling bundled linux tools. [07:48:02] Found bwa - /usr/local/bin/bwa [07:48:02] Found bcftools - /usr/local/bin/bcftools [07:48:02] Found samtools - /usr/local/bin/samtools [07:48:02] Found java - /usr/local/bin/java [07:48:02] Found snpEff - /usr/local/bin/snpEff [07:48:02] Found samclip - /usr/local/bin/samclip [07:48:02] Found seqtk - /usr/local/bin/seqtk [07:48:02] Found parallel - /usr/local/bin/parallel [07:48:02] Found freebayes - /usr/local/bin/freebayes [07:48:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:48:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:48:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:48:02] Found vcfuniq - /usr/local/bin/vcfuniq [07:48:02] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:48:02] Found gzip - /bin/gzip [07:48:02] Found vt - /usr/local/bin/vt [07:48:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:48:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:48:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:48:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:48:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:48:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:48:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:48:03] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:48:14] This is snippy 4.6.0
Show full stderr[07:48:14] This is snippy 4.6.0 [07:48:14] Written by Torsten Seemann [07:48:14] Obtained from https://github.com/tseemann/snippy [07:48:14] Detected operating system: linux [07:48:14] Enabling bundled linux tools. [07:48:14] Found bwa - /usr/local/bin/bwa [07:48:14] Found bcftools - /usr/local/bin/bcftools [07:48:14] Found samtools - /usr/local/bin/samtools [07:48:14] Found java - /usr/local/bin/java [07:48:14] Found snpEff - /usr/local/bin/snpEff [07:48:14] Found samclip - /usr/local/bin/samclip [07:48:14] Found seqtk - /usr/local/bin/seqtk [07:48:14] Found parallel - /usr/local/bin/parallel [07:48:14] Found freebayes - /usr/local/bin/freebayes [07:48:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:48:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:48:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:48:14] Found vcfuniq - /usr/local/bin/vcfuniq [07:48:14] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:48:14] Found gzip - /bin/gzip [07:48:14] Found vt - /usr/local/bin/vt [07:48:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:48:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:48:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:48:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:48:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:48:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:48:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:48:15] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:48:17] This is snippy 4.6.0
Show full stderr[07:48:17] This is snippy 4.6.0 [07:48:17] Written by Torsten Seemann [07:48:17] Obtained from https://github.com/tseemann/snippy [07:48:17] Detected operating system: linux [07:48:17] Enabling bundled linux tools. [07:48:17] Found bwa - /usr/local/bin/bwa [07:48:17] Found bcftools - /usr/local/bin/bcftools [07:48:17] Found samtools - /usr/local/bin/samtools [07:48:17] Found java - /usr/local/bin/java [07:48:17] Found snpEff - /usr/local/bin/snpEff [07:48:17] Found samclip - /usr/local/bin/samclip [07:48:17] Found seqtk - /usr/local/bin/seqtk [07:48:17] Found parallel - /usr/local/bin/parallel [07:48:17] Found freebayes - /usr/local/bin/freebayes [07:48:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:48:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:48:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:48:17] Found vcfuniq - /usr/local/bin/vcfuniq [07:48:17] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:48:17] Found gzip - /bin/gzip [07:48:17] Found vt - /usr/local/bin/vt [07:48:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:48:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:48:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:48:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:48:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:48:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:48:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:48:18] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:42:52] This is snippy 4.6.0
Show full stderr[07:42:52] This is snippy 4.6.0 [07:42:52] Written by Torsten Seemann [07:42:52] Obtained from https://github.com/tseemann/snippy [07:42:52] Detected operating system: linux [07:42:52] Enabling bundled linux tools. [07:42:52] Found bwa - /usr/local/bin/bwa [07:42:52] Found bcftools - /usr/local/bin/bcftools [07:42:52] Found samtools - /usr/local/bin/samtools [07:42:52] Found java - /usr/local/bin/java [07:42:52] Found snpEff - /usr/local/bin/snpEff [07:42:52] Found samclip - /usr/local/bin/samclip [07:42:52] Found seqtk - /usr/local/bin/seqtk [07:42:52] Found parallel - /usr/local/bin/parallel [07:42:52] Found freebayes - /usr/local/bin/freebayes [07:42:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:42:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:42:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:42:52] Found vcfuniq - /usr/local/bin/vcfuniq [07:42:52] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:42:52] Found gzip - /bin/gzip [07:42:52] Found vt - /usr/local/bin/vt [07:42:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:42:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:42:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:42:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:42:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:42:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:42:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:42:53] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:43:34] This is snippy 4.6.0
Show full stderr[07:43:34] This is snippy 4.6.0 [07:43:34] Written by Torsten Seemann [07:43:34] Obtained from https://github.com/tseemann/snippy [07:43:34] Detected operating system: linux [07:43:34] Enabling bundled linux tools. [07:43:34] Found bwa - /usr/local/bin/bwa [07:43:34] Found bcftools - /usr/local/bin/bcftools [07:43:34] Found samtools - /usr/local/bin/samtools [07:43:34] Found java - /usr/local/bin/java [07:43:34] Found snpEff - /usr/local/bin/snpEff [07:43:34] Found samclip - /usr/local/bin/samclip [07:43:34] Found seqtk - /usr/local/bin/seqtk [07:43:34] Found parallel - /usr/local/bin/parallel [07:43:34] Found freebayes - /usr/local/bin/freebayes [07:43:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:43:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:43:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:43:34] Found vcfuniq - /usr/local/bin/vcfuniq [07:43:34] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:43:34] Found gzip - /bin/gzip [07:43:34] Found vt - /usr/local/bin/vt [07:43:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:43:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:43:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:43:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:43:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:43:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:43:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:43:35] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:43:51] This is snippy 4.6.0
Show full stderr[07:43:51] This is snippy 4.6.0 [07:43:51] Written by Torsten Seemann [07:43:51] Obtained from https://github.com/tseemann/snippy [07:43:51] Detected operating system: linux [07:43:51] Enabling bundled linux tools. [07:43:51] Found bwa - /usr/local/bin/bwa [07:43:51] Found bcftools - /usr/local/bin/bcftools [07:43:51] Found samtools - /usr/local/bin/samtools [07:43:51] Found java - /usr/local/bin/java [07:43:51] Found snpEff - /usr/local/bin/snpEff [07:43:51] Found samclip - /usr/local/bin/samclip [07:43:51] Found seqtk - /usr/local/bin/seqtk [07:43:51] Found parallel - /usr/local/bin/parallel [07:43:51] Found freebayes - /usr/local/bin/freebayes [07:43:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:43:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:43:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:43:51] Found vcfuniq - /usr/local/bin/vcfuniq [07:43:51] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:43:51] Found gzip - /bin/gzip [07:43:51] Found vt - /usr/local/bin/vt [07:43:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:43:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:43:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:43:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:43:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:43:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:43:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:43:52] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:44:07] This is snippy 4.6.0
Show full stderr[07:44:07] This is snippy 4.6.0 [07:44:07] Written by Torsten Seemann [07:44:07] Obtained from https://github.com/tseemann/snippy [07:44:07] Detected operating system: linux [07:44:07] Enabling bundled linux tools. [07:44:07] Found bwa - /usr/local/bin/bwa [07:44:07] Found bcftools - /usr/local/bin/bcftools [07:44:07] Found samtools - /usr/local/bin/samtools [07:44:07] Found java - /usr/local/bin/java [07:44:07] Found snpEff - /usr/local/bin/snpEff [07:44:07] Found samclip - /usr/local/bin/samclip [07:44:07] Found seqtk - /usr/local/bin/seqtk [07:44:07] Found parallel - /usr/local/bin/parallel [07:44:07] Found freebayes - /usr/local/bin/freebayes [07:44:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:44:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:44:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:44:07] Found vcfuniq - /usr/local/bin/vcfuniq [07:44:07] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:44:07] Found gzip - /bin/gzip [07:44:07] Found vt - /usr/local/bin/vt [07:44:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:44:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:44:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:44:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:44:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:44:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:44:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:44:08] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:44:31] This is snippy 4.6.0
Show full stderr[07:44:31] This is snippy 4.6.0 [07:44:31] Written by Torsten Seemann [07:44:31] Obtained from https://github.com/tseemann/snippy [07:44:31] Detected operating system: linux [07:44:31] Enabling bundled linux tools. [07:44:31] Found bwa - /usr/local/bin/bwa [07:44:31] Found bcftools - /usr/local/bin/bcftools [07:44:31] Found samtools - /usr/local/bin/samtools [07:44:31] Found java - /usr/local/bin/java [07:44:31] Found snpEff - /usr/local/bin/snpEff [07:44:31] Found samclip - /usr/local/bin/samclip [07:44:31] Found seqtk - /usr/local/bin/seqtk [07:44:31] Found parallel - /usr/local/bin/parallel [07:44:31] Found freebayes - /usr/local/bin/freebayes [07:44:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:44:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:44:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:44:31] Found vcfuniq - /usr/local/bin/vcfuniq [07:44:31] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:44:31] Found gzip - /bin/gzip [07:44:31] Found vt - /usr/local/bin/vt [07:44:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:44:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:44:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:44:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:44:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:44:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:44:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:44:32] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:48:53] This is snippy 4.6.0
Show full stderr[07:48:53] This is snippy 4.6.0 [07:48:53] Written by Torsten Seemann [07:48:53] Obtained from https://github.com/tseemann/snippy [07:48:53] Detected operating system: linux [07:48:53] Enabling bundled linux tools. [07:48:53] Found bwa - /usr/local/bin/bwa [07:48:53] Found bcftools - /usr/local/bin/bcftools [07:48:53] Found samtools - /usr/local/bin/samtools [07:48:53] Found java - /usr/local/bin/java [07:48:53] Found snpEff - /usr/local/bin/snpEff [07:48:53] Found samclip - /usr/local/bin/samclip [07:48:53] Found seqtk - /usr/local/bin/seqtk [07:48:53] Found parallel - /usr/local/bin/parallel [07:48:53] Found freebayes - /usr/local/bin/freebayes [07:48:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:48:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:48:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:48:53] Found vcfuniq - /usr/local/bin/vcfuniq [07:48:53] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:48:53] Found gzip - /bin/gzip [07:48:53] Found vt - /usr/local/bin/vt [07:48:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:48:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:48:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:48:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:48:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:48:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:48:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:48:54] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:48:59] This is snippy 4.6.0
Show full stderr[07:48:59] This is snippy 4.6.0 [07:48:59] Written by Torsten Seemann [07:48:59] Obtained from https://github.com/tseemann/snippy [07:48:59] Detected operating system: linux [07:48:59] Enabling bundled linux tools. [07:48:59] Found bwa - /usr/local/bin/bwa [07:48:59] Found bcftools - /usr/local/bin/bcftools [07:48:59] Found samtools - /usr/local/bin/samtools [07:48:59] Found java - /usr/local/bin/java [07:48:59] Found snpEff - /usr/local/bin/snpEff [07:48:59] Found samclip - /usr/local/bin/samclip [07:48:59] Found seqtk - /usr/local/bin/seqtk [07:48:59] Found parallel - /usr/local/bin/parallel [07:48:59] Found freebayes - /usr/local/bin/freebayes [07:48:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:48:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:48:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:48:59] Found vcfuniq - /usr/local/bin/vcfuniq [07:48:59] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:48:59] Found gzip - /bin/gzip [07:48:59] Found vt - /usr/local/bin/vt [07:48:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:48:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:48:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:48:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:48:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:49:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:49:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:49:00] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:49:07] This is snippy 4.6.0
Show full stderr[07:49:07] This is snippy 4.6.0 [07:49:07] Written by Torsten Seemann [07:49:07] Obtained from https://github.com/tseemann/snippy [07:49:07] Detected operating system: linux [07:49:07] Enabling bundled linux tools. [07:49:07] Found bwa - /usr/local/bin/bwa [07:49:07] Found bcftools - /usr/local/bin/bcftools [07:49:07] Found samtools - /usr/local/bin/samtools [07:49:07] Found java - /usr/local/bin/java [07:49:07] Found snpEff - /usr/local/bin/snpEff [07:49:07] Found samclip - /usr/local/bin/samclip [07:49:07] Found seqtk - /usr/local/bin/seqtk [07:49:07] Found parallel - /usr/local/bin/parallel [07:49:07] Found freebayes - /usr/local/bin/freebayes [07:49:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:49:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:49:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:49:07] Found vcfuniq - /usr/local/bin/vcfuniq [07:49:07] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:49:07] Found gzip - /bin/gzip [07:49:07] Found vt - /usr/local/bin/vt [07:49:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:49:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:49:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:49:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:49:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:49:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:49:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:49:08] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:49:13] This is snippy 4.6.0
Show full stderr[07:49:13] This is snippy 4.6.0 [07:49:13] Written by Torsten Seemann [07:49:13] Obtained from https://github.com/tseemann/snippy [07:49:13] Detected operating system: linux [07:49:13] Enabling bundled linux tools. [07:49:13] Found bwa - /usr/local/bin/bwa [07:49:13] Found bcftools - /usr/local/bin/bcftools [07:49:13] Found samtools - /usr/local/bin/samtools [07:49:13] Found java - /usr/local/bin/java [07:49:13] Found snpEff - /usr/local/bin/snpEff [07:49:13] Found samclip - /usr/local/bin/samclip [07:49:13] Found seqtk - /usr/local/bin/seqtk [07:49:13] Found parallel - /usr/local/bin/parallel [07:49:13] Found freebayes - /usr/local/bin/freebayes [07:49:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:49:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:49:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:49:13] Found vcfuniq - /usr/local/bin/vcfuniq [07:49:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:49:13] Found gzip - /bin/gzip [07:49:13] Found vt - /usr/local/bin/vt [07:49:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:49:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:49:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:49:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:49:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:49:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:49:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:49:14] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:49:22] This is snippy 4.6.0
Show full stderr[07:49:22] This is snippy 4.6.0 [07:49:22] Written by Torsten Seemann [07:49:22] Obtained from https://github.com/tseemann/snippy [07:49:22] Detected operating system: linux [07:49:22] Enabling bundled linux tools. [07:49:22] Found bwa - /usr/local/bin/bwa [07:49:22] Found bcftools - /usr/local/bin/bcftools [07:49:22] Found samtools - /usr/local/bin/samtools [07:49:22] Found java - /usr/local/bin/java [07:49:22] Found snpEff - /usr/local/bin/snpEff [07:49:22] Found samclip - /usr/local/bin/samclip [07:49:22] Found seqtk - /usr/local/bin/seqtk [07:49:22] Found parallel - /usr/local/bin/parallel [07:49:22] Found freebayes - /usr/local/bin/freebayes [07:49:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:49:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:49:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:49:22] Found vcfuniq - /usr/local/bin/vcfuniq [07:49:22] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:49:22] Found gzip - /bin/gzip [07:49:22] Found vt - /usr/local/bin/vt [07:49:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:49:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:49:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:49:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:49:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:49:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:49:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:49:23] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:49:28] This is snippy 4.6.0
Show full stderr[07:49:28] This is snippy 4.6.0 [07:49:28] Written by Torsten Seemann [07:49:28] Obtained from https://github.com/tseemann/snippy [07:49:28] Detected operating system: linux [07:49:28] Enabling bundled linux tools. [07:49:28] Found bwa - /usr/local/bin/bwa [07:49:28] Found bcftools - /usr/local/bin/bcftools [07:49:28] Found samtools - /usr/local/bin/samtools [07:49:28] Found java - /usr/local/bin/java [07:49:28] Found snpEff - /usr/local/bin/snpEff [07:49:28] Found samclip - /usr/local/bin/samclip [07:49:28] Found seqtk - /usr/local/bin/seqtk [07:49:28] Found parallel - /usr/local/bin/parallel [07:49:28] Found freebayes - /usr/local/bin/freebayes [07:49:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:49:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:49:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:49:28] Found vcfuniq - /usr/local/bin/vcfuniq [07:49:28] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:49:28] Found gzip - /bin/gzip [07:49:28] Found vt - /usr/local/bin/vt [07:49:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:49:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:49:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:49:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:49:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:49:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:49:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:49:29] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:49:37] This is snippy 4.6.0
Show full stderr[07:49:37] This is snippy 4.6.0 [07:49:37] Written by Torsten Seemann [07:49:37] Obtained from https://github.com/tseemann/snippy [07:49:37] Detected operating system: linux [07:49:37] Enabling bundled linux tools. [07:49:37] Found bwa - /usr/local/bin/bwa [07:49:37] Found bcftools - /usr/local/bin/bcftools [07:49:37] Found samtools - /usr/local/bin/samtools [07:49:37] Found java - /usr/local/bin/java [07:49:37] Found snpEff - /usr/local/bin/snpEff [07:49:37] Found samclip - /usr/local/bin/samclip [07:49:37] Found seqtk - /usr/local/bin/seqtk [07:49:37] Found parallel - /usr/local/bin/parallel [07:49:37] Found freebayes - /usr/local/bin/freebayes [07:49:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:49:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:49:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:49:37] Found vcfuniq - /usr/local/bin/vcfuniq [07:49:37] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:49:37] Found gzip - /bin/gzip [07:49:37] Found vt - /usr/local/bin/vt [07:49:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:49:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:49:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:49:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:49:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:49:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:49:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:49:38] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:49:40] This is snippy 4.6.0
Show full stderr[07:49:40] This is snippy 4.6.0 [07:49:40] Written by Torsten Seemann [07:49:40] Obtained from https://github.com/tseemann/snippy [07:49:40] Detected operating system: linux [07:49:40] Enabling bundled linux tools. [07:49:40] Found bwa - /usr/local/bin/bwa [07:49:40] Found bcftools - /usr/local/bin/bcftools [07:49:40] Found samtools - /usr/local/bin/samtools [07:49:40] Found java - /usr/local/bin/java [07:49:40] Found snpEff - /usr/local/bin/snpEff [07:49:40] Found samclip - /usr/local/bin/samclip [07:49:40] Found seqtk - /usr/local/bin/seqtk [07:49:40] Found parallel - /usr/local/bin/parallel [07:49:40] Found freebayes - /usr/local/bin/freebayes [07:49:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:49:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:49:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:49:40] Found vcfuniq - /usr/local/bin/vcfuniq [07:49:40] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:49:40] Found gzip - /bin/gzip [07:49:40] Found vt - /usr/local/bin/vt [07:49:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:49:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:49:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:49:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:49:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:49:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:49:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:49:41] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:49:49] This is snippy 4.6.0
Show full stderr[07:49:49] This is snippy 4.6.0 [07:49:49] Written by Torsten Seemann [07:49:49] Obtained from https://github.com/tseemann/snippy [07:49:49] Detected operating system: linux [07:49:49] Enabling bundled linux tools. [07:49:49] Found bwa - /usr/local/bin/bwa [07:49:49] Found bcftools - /usr/local/bin/bcftools [07:49:49] Found samtools - /usr/local/bin/samtools [07:49:49] Found java - /usr/local/bin/java [07:49:49] Found snpEff - /usr/local/bin/snpEff [07:49:49] Found samclip - /usr/local/bin/samclip [07:49:49] Found seqtk - /usr/local/bin/seqtk [07:49:49] Found parallel - /usr/local/bin/parallel [07:49:49] Found freebayes - /usr/local/bin/freebayes [07:49:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:49:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:49:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:49:49] Found vcfuniq - /usr/local/bin/vcfuniq [07:49:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:49:49] Found gzip - /bin/gzip [07:49:49] Found vt - /usr/local/bin/vt [07:49:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:49:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:49:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:49:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:49:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:49:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:49:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:49:50] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:45:19] This is snippy 4.6.0
Show full stderr[07:45:19] This is snippy 4.6.0 [07:45:19] Written by Torsten Seemann [07:45:19] Obtained from https://github.com/tseemann/snippy [07:45:19] Detected operating system: linux [07:45:19] Enabling bundled linux tools. [07:45:19] Found bwa - /usr/local/bin/bwa [07:45:19] Found bcftools - /usr/local/bin/bcftools [07:45:19] Found samtools - /usr/local/bin/samtools [07:45:19] Found java - /usr/local/bin/java [07:45:19] Found snpEff - /usr/local/bin/snpEff [07:45:19] Found samclip - /usr/local/bin/samclip [07:45:19] Found seqtk - /usr/local/bin/seqtk [07:45:19] Found parallel - /usr/local/bin/parallel [07:45:19] Found freebayes - /usr/local/bin/freebayes [07:45:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:45:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:45:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:45:19] Found vcfuniq - /usr/local/bin/vcfuniq [07:45:19] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:45:19] Found gzip - /bin/gzip [07:45:19] Found vt - /usr/local/bin/vt [07:45:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:45:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:45:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:45:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:45:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:45:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:45:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:45:20] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:45:28] This is snippy 4.6.0
Show full stderr[07:45:28] This is snippy 4.6.0 [07:45:28] Written by Torsten Seemann [07:45:28] Obtained from https://github.com/tseemann/snippy [07:45:28] Detected operating system: linux [07:45:28] Enabling bundled linux tools. [07:45:28] Found bwa - /usr/local/bin/bwa [07:45:28] Found bcftools - /usr/local/bin/bcftools [07:45:28] Found samtools - /usr/local/bin/samtools [07:45:28] Found java - /usr/local/bin/java [07:45:28] Found snpEff - /usr/local/bin/snpEff [07:45:28] Found samclip - /usr/local/bin/samclip [07:45:28] Found seqtk - /usr/local/bin/seqtk [07:45:28] Found parallel - /usr/local/bin/parallel [07:45:28] Found freebayes - /usr/local/bin/freebayes [07:45:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:45:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:45:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:45:28] Found vcfuniq - /usr/local/bin/vcfuniq [07:45:28] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:45:28] Found gzip - /bin/gzip [07:45:28] Found vt - /usr/local/bin/vt [07:45:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:45:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:45:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:45:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:45:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:45:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:45:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:45:29] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:45:37] This is snippy 4.6.0
Show full stderr[07:45:37] This is snippy 4.6.0 [07:45:37] Written by Torsten Seemann [07:45:37] Obtained from https://github.com/tseemann/snippy [07:45:37] Detected operating system: linux [07:45:37] Enabling bundled linux tools. [07:45:37] Found bwa - /usr/local/bin/bwa [07:45:37] Found bcftools - /usr/local/bin/bcftools [07:45:37] Found samtools - /usr/local/bin/samtools [07:45:37] Found java - /usr/local/bin/java [07:45:37] Found snpEff - /usr/local/bin/snpEff [07:45:37] Found samclip - /usr/local/bin/samclip [07:45:37] Found seqtk - /usr/local/bin/seqtk [07:45:37] Found parallel - /usr/local/bin/parallel [07:45:37] Found freebayes - /usr/local/bin/freebayes [07:45:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:45:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:45:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:45:37] Found vcfuniq - /usr/local/bin/vcfuniq [07:45:37] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:45:37] Found gzip - /bin/gzip [07:45:37] Found vt - /usr/local/bin/vt [07:45:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:45:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:45:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:45:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:45:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:45:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:45:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:45:38] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:45:43] This is snippy 4.6.0
Show full stderr[07:45:43] This is snippy 4.6.0 [07:45:43] Written by Torsten Seemann [07:45:43] Obtained from https://github.com/tseemann/snippy [07:45:43] Detected operating system: linux [07:45:43] Enabling bundled linux tools. [07:45:43] Found bwa - /usr/local/bin/bwa [07:45:43] Found bcftools - /usr/local/bin/bcftools [07:45:43] Found samtools - /usr/local/bin/samtools [07:45:43] Found java - /usr/local/bin/java [07:45:43] Found snpEff - /usr/local/bin/snpEff [07:45:43] Found samclip - /usr/local/bin/samclip [07:45:43] Found seqtk - /usr/local/bin/seqtk [07:45:43] Found parallel - /usr/local/bin/parallel [07:45:43] Found freebayes - /usr/local/bin/freebayes [07:45:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:45:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:45:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:45:43] Found vcfuniq - /usr/local/bin/vcfuniq [07:45:43] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:45:43] Found gzip - /bin/gzip [07:45:43] Found vt - /usr/local/bin/vt [07:45:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:45:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:45:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:45:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:45:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:45:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:45:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:45:44] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:45:46] This is snippy 4.6.0
Show full stderr[07:45:46] This is snippy 4.6.0 [07:45:46] Written by Torsten Seemann [07:45:46] Obtained from https://github.com/tseemann/snippy [07:45:46] Detected operating system: linux [07:45:46] Enabling bundled linux tools. [07:45:46] Found bwa - /usr/local/bin/bwa [07:45:46] Found bcftools - /usr/local/bin/bcftools [07:45:46] Found samtools - /usr/local/bin/samtools [07:45:46] Found java - /usr/local/bin/java [07:45:46] Found snpEff - /usr/local/bin/snpEff [07:45:46] Found samclip - /usr/local/bin/samclip [07:45:46] Found seqtk - /usr/local/bin/seqtk [07:45:46] Found parallel - /usr/local/bin/parallel [07:45:46] Found freebayes - /usr/local/bin/freebayes [07:45:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:45:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:45:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:45:46] Found vcfuniq - /usr/local/bin/vcfuniq [07:45:46] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:45:46] Found gzip - /bin/gzip [07:45:46] Found vt - /usr/local/bin/vt [07:45:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:45:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:45:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:45:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:45:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:45:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:45:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:45:47] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:45:49] This is snippy 4.6.0
Show full stderr[07:45:49] This is snippy 4.6.0 [07:45:49] Written by Torsten Seemann [07:45:49] Obtained from https://github.com/tseemann/snippy [07:45:49] Detected operating system: linux [07:45:49] Enabling bundled linux tools. [07:45:49] Found bwa - /usr/local/bin/bwa [07:45:49] Found bcftools - /usr/local/bin/bcftools [07:45:49] Found samtools - /usr/local/bin/samtools [07:45:49] Found java - /usr/local/bin/java [07:45:49] Found snpEff - /usr/local/bin/snpEff [07:45:49] Found samclip - /usr/local/bin/samclip [07:45:49] Found seqtk - /usr/local/bin/seqtk [07:45:49] Found parallel - /usr/local/bin/parallel [07:45:49] Found freebayes - /usr/local/bin/freebayes [07:45:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:45:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:45:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:45:49] Found vcfuniq - /usr/local/bin/vcfuniq [07:45:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:45:49] Found gzip - /bin/gzip [07:45:49] Found vt - /usr/local/bin/vt [07:45:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:45:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:45:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:45:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:45:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:45:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:45:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:45:50] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:45:52] This is snippy 4.6.0
Show full stderr[07:45:52] This is snippy 4.6.0 [07:45:52] Written by Torsten Seemann [07:45:52] Obtained from https://github.com/tseemann/snippy [07:45:52] Detected operating system: linux [07:45:52] Enabling bundled linux tools. [07:45:52] Found bwa - /usr/local/bin/bwa [07:45:52] Found bcftools - /usr/local/bin/bcftools [07:45:52] Found samtools - /usr/local/bin/samtools [07:45:52] Found java - /usr/local/bin/java [07:45:52] Found snpEff - /usr/local/bin/snpEff [07:45:52] Found samclip - /usr/local/bin/samclip [07:45:52] Found seqtk - /usr/local/bin/seqtk [07:45:52] Found parallel - /usr/local/bin/parallel [07:45:52] Found freebayes - /usr/local/bin/freebayes [07:45:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:45:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:45:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:45:52] Found vcfuniq - /usr/local/bin/vcfuniq [07:45:52] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:45:52] Found gzip - /bin/gzip [07:45:52] Found vt - /usr/local/bin/vt [07:45:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:45:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:45:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:45:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:45:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:45:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:45:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:45:53] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:45:58] This is snippy 4.6.0
Show full stderr[07:45:58] This is snippy 4.6.0 [07:45:58] Written by Torsten Seemann [07:45:58] Obtained from https://github.com/tseemann/snippy [07:45:58] Detected operating system: linux [07:45:58] Enabling bundled linux tools. [07:45:58] Found bwa - /usr/local/bin/bwa [07:45:58] Found bcftools - /usr/local/bin/bcftools [07:45:58] Found samtools - /usr/local/bin/samtools [07:45:58] Found java - /usr/local/bin/java [07:45:58] Found snpEff - /usr/local/bin/snpEff [07:45:58] Found samclip - /usr/local/bin/samclip [07:45:58] Found seqtk - /usr/local/bin/seqtk [07:45:58] Found parallel - /usr/local/bin/parallel [07:45:58] Found freebayes - /usr/local/bin/freebayes [07:45:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:45:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:45:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:45:58] Found vcfuniq - /usr/local/bin/vcfuniq [07:45:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:45:58] Found gzip - /bin/gzip [07:45:58] Found vt - /usr/local/bin/vt [07:45:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:45:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:45:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:45:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:45:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:45:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:45:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:45:59] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:46:13] This is snippy 4.6.0
Show full stderr[07:46:13] This is snippy 4.6.0 [07:46:13] Written by Torsten Seemann [07:46:13] Obtained from https://github.com/tseemann/snippy [07:46:13] Detected operating system: linux [07:46:13] Enabling bundled linux tools. [07:46:13] Found bwa - /usr/local/bin/bwa [07:46:13] Found bcftools - /usr/local/bin/bcftools [07:46:13] Found samtools - /usr/local/bin/samtools [07:46:13] Found java - /usr/local/bin/java [07:46:13] Found snpEff - /usr/local/bin/snpEff [07:46:13] Found samclip - /usr/local/bin/samclip [07:46:13] Found seqtk - /usr/local/bin/seqtk [07:46:13] Found parallel - /usr/local/bin/parallel [07:46:13] Found freebayes - /usr/local/bin/freebayes [07:46:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:46:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:46:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:46:13] Found vcfuniq - /usr/local/bin/vcfuniq [07:46:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:46:13] Found gzip - /bin/gzip [07:46:13] Found vt - /usr/local/bin/vt [07:46:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:46:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:46:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:46:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:46:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:46:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:46:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:46:14] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:46:28] This is snippy 4.6.0
Show full stderr[07:46:28] This is snippy 4.6.0 [07:46:28] Written by Torsten Seemann [07:46:28] Obtained from https://github.com/tseemann/snippy [07:46:28] Detected operating system: linux [07:46:28] Enabling bundled linux tools. [07:46:28] Found bwa - /usr/local/bin/bwa [07:46:28] Found bcftools - /usr/local/bin/bcftools [07:46:28] Found samtools - /usr/local/bin/samtools [07:46:28] Found java - /usr/local/bin/java [07:46:28] Found snpEff - /usr/local/bin/snpEff [07:46:28] Found samclip - /usr/local/bin/samclip [07:46:28] Found seqtk - /usr/local/bin/seqtk [07:46:28] Found parallel - /usr/local/bin/parallel [07:46:28] Found freebayes - /usr/local/bin/freebayes [07:46:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:46:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:46:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:46:28] Found vcfuniq - /usr/local/bin/vcfuniq [07:46:28] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:46:28] Found gzip - /bin/gzip [07:46:28] Found vt - /usr/local/bin/vt [07:46:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:46:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:46:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:46:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:46:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:46:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:46:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:46:29] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:46:46] This is snippy 4.6.0
Show full stderr[07:46:46] This is snippy 4.6.0 [07:46:46] Written by Torsten Seemann [07:46:46] Obtained from https://github.com/tseemann/snippy [07:46:46] Detected operating system: linux [07:46:46] Enabling bundled linux tools. [07:46:46] Found bwa - /usr/local/bin/bwa [07:46:46] Found bcftools - /usr/local/bin/bcftools [07:46:46] Found samtools - /usr/local/bin/samtools [07:46:46] Found java - /usr/local/bin/java [07:46:46] Found snpEff - /usr/local/bin/snpEff [07:46:46] Found samclip - /usr/local/bin/samclip [07:46:46] Found seqtk - /usr/local/bin/seqtk [07:46:46] Found parallel - /usr/local/bin/parallel [07:46:46] Found freebayes - /usr/local/bin/freebayes [07:46:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:46:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:46:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:46:46] Found vcfuniq - /usr/local/bin/vcfuniq [07:46:46] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:46:46] Found gzip - /bin/gzip [07:46:46] Found vt - /usr/local/bin/vt [07:46:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:46:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:46:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:46:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:46:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:46:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:46:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:46:47] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:46:49] This is snippy 4.6.0
Show full stderr[07:46:49] This is snippy 4.6.0 [07:46:49] Written by Torsten Seemann [07:46:49] Obtained from https://github.com/tseemann/snippy [07:46:49] Detected operating system: linux [07:46:49] Enabling bundled linux tools. [07:46:49] Found bwa - /usr/local/bin/bwa [07:46:49] Found bcftools - /usr/local/bin/bcftools [07:46:49] Found samtools - /usr/local/bin/samtools [07:46:49] Found java - /usr/local/bin/java [07:46:49] Found snpEff - /usr/local/bin/snpEff [07:46:49] Found samclip - /usr/local/bin/samclip [07:46:49] Found seqtk - /usr/local/bin/seqtk [07:46:49] Found parallel - /usr/local/bin/parallel [07:46:49] Found freebayes - /usr/local/bin/freebayes [07:46:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:46:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:46:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:46:49] Found vcfuniq - /usr/local/bin/vcfuniq [07:46:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:46:49] Found gzip - /bin/gzip [07:46:49] Found vt - /usr/local/bin/vt [07:46:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:46:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:46:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:46:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:46:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:46:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:46:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:46:50] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:47:01] This is snippy 4.6.0
Show full stderr[07:47:01] This is snippy 4.6.0 [07:47:01] Written by Torsten Seemann [07:47:01] Obtained from https://github.com/tseemann/snippy [07:47:01] Detected operating system: linux [07:47:01] Enabling bundled linux tools. [07:47:01] Found bwa - /usr/local/bin/bwa [07:47:01] Found bcftools - /usr/local/bin/bcftools [07:47:01] Found samtools - /usr/local/bin/samtools [07:47:01] Found java - /usr/local/bin/java [07:47:01] Found snpEff - /usr/local/bin/snpEff [07:47:01] Found samclip - /usr/local/bin/samclip [07:47:01] Found seqtk - /usr/local/bin/seqtk [07:47:01] Found parallel - /usr/local/bin/parallel [07:47:01] Found freebayes - /usr/local/bin/freebayes [07:47:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:47:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:47:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:47:01] Found vcfuniq - /usr/local/bin/vcfuniq [07:47:01] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:47:01] Found gzip - /bin/gzip [07:47:01] Found vt - /usr/local/bin/vt [07:47:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:47:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:47:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:47:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:47:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:47:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:47:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:47:02] Please supply a reference FASTA/GBK/EMBL file with --reference
1[08:22:28] This is snippy 4.6.0
Show full stderr[08:22:28] This is snippy 4.6.0 [08:22:28] Written by Torsten Seemann [08:22:28] Obtained from https://github.com/tseemann/snippy [08:22:28] Detected operating system: linux [08:22:28] Enabling bundled linux tools. [08:22:28] Found bwa - /usr/local/bin/bwa [08:22:28] Found bcftools - /usr/local/bin/bcftools [08:22:28] Found samtools - /usr/local/bin/samtools [08:22:28] Found java - /usr/local/bin/java [08:22:28] Found snpEff - /usr/local/bin/snpEff [08:22:28] Found samclip - /usr/local/bin/samclip [08:22:28] Found seqtk - /usr/local/bin/seqtk [08:22:28] Found parallel - /usr/local/bin/parallel [08:22:28] Found freebayes - /usr/local/bin/freebayes [08:22:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:22:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:22:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:22:28] Found vcfuniq - /usr/local/bin/vcfuniq [08:22:28] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:22:28] Found gzip - /bin/gzip [08:22:28] Found vt - /usr/local/bin/vt [08:22:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:22:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:22:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:22:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:22:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:22:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:22:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:22:29] Using reference: /corral4/main/objects/b/2/e/dataset_b2e63dfb-6861-4d9c-a497-0b231c9ac46a.dat [08:22:29] Treating reference as 'fasta' format. [08:22:29] Will use 1 CPU cores. [08:22:29] Using read file: /corral4/main/objects/4/7/b/dataset_47b089a5-7ccc-49f2-b505-f2adb97b524c.dat [08:22:29] Creating folder: Resistance_93_fasta [08:22:29] Changing working directory: Resistance_93_fasta [08:22:29] Creating reference folder: reference [08:22:29] Extracting FASTA and GFF from reference. [08:22:29] Wrote 1 sequences to ref.fa [08:22:29] Wrote 0 features to ref.gff [08:22:29] Shredding /corral4/main/objects/4/7/b/dataset_47b089a5-7ccc-49f2-b505-f2adb97b524c.dat into pseudo-reads [08:22:33] Wrote 422488 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [08:22:33] Freebayes will process 1 chunks of 3047 bp, 1 chunks at a time. [08:22:33] Using BAM RG (Read Group) ID: Resistance_93_fasta [08:22:33] Running: samtools faidx reference/ref.fa 2>> snps.log [08:22:33] Running: bwa index reference/ref.fa 2>> snps.log [08:22:33] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [08:22:33] Running: ln -sf reference/ref.fa . 2>> snps.log [08:22:33] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [08:22:33] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [08:22:33] Running: bwa mem -Y -M -R '@RG\tID:Resistance_93_fasta\tSM:Resistance_93_fasta' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/264/72264696/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/264/72264696/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/264/72264696/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 1 sequences in reference/ref.fa.fai [M::process]
1[09:20:22] This is snippy 4.6.0
Show full stderr[09:20:22] This is snippy 4.6.0 [09:20:22] Written by Torsten Seemann [09:20:22] Obtained from https://github.com/tseemann/snippy [09:20:22] Detected operating system: linux [09:20:22] Enabling bundled linux tools. [09:20:22] Found bwa - /usr/local/bin/bwa [09:20:22] Found bcftools - /usr/local/bin/bcftools [09:20:22] Found samtools - /usr/local/bin/samtools [09:20:22] Found java - /usr/local/bin/java [09:20:22] Found snpEff - /usr/local/bin/snpEff [09:20:22] Found samclip - /usr/local/bin/samclip [09:20:22] Found seqtk - /usr/local/bin/seqtk [09:20:22] Found parallel - /usr/local/bin/parallel [09:20:22] Found freebayes - /usr/local/bin/freebayes [09:20:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [09:20:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [09:20:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [09:20:22] Found vcfuniq - /usr/local/bin/vcfuniq [09:20:22] Found vcffirstheader - /usr/local/bin/vcffirstheader [09:20:22] Found gzip - /bin/gzip [09:20:22] Found vt - /usr/local/bin/vt [09:20:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [09:20:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [09:20:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [09:20:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [09:20:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [09:20:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [09:20:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [09:20:22] Using reference: /cvmfs/data.galaxyproject.org/byhand/Araly1/seq/Araly1.fa [09:20:23] Treating reference as 'fasta' format. [09:20:23] Will use 1 CPU cores. [09:20:23] Using read file: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat [09:20:23] Using read file: /corral4/main/objects/b/3/d/dataset_b3d4e3f0-7686-4f07-83e7-d370bd805280.dat [09:20:23] Creating folder: GCF_000195955_2_ASM19595v2_genomic_fna [09:20:23] Changing working directory: GCF_000195955_2_ASM19595v2_genomic_fna [09:20:23] Creating reference folder: reference [09:20:23] Extracting FASTA and GFF from reference. [09:20:31] Wrote 702 sequences to ref.fa [09:20:31] Wrote 0 features to ref.gff [09:20:31] Freebayes will process 1 chunks of 210374351 bp, 1 chunks at a time. [09:20:31] Using BAM RG (Read Group) ID: GCF_000195955_2_ASM19595v2_genomic_fna [09:20:31] Running: samtools faidx reference/ref.fa 2>> snps.log [09:20:32] Error running command, check GCF_000195955_2_ASM19595v2_genomic_fna/snps.log
1[09:30:00] This is snippy 4.6.0
Show full stderr[09:30:00] This is snippy 4.6.0 [09:30:00] Written by Torsten Seemann [09:30:00] Obtained from https://github.com/tseemann/snippy [09:30:00] Detected operating system: linux [09:30:00] Enabling bundled linux tools. [09:30:00] Found bwa - /usr/local/bin/bwa [09:30:00] Found bcftools - /usr/local/bin/bcftools [09:30:00] Found samtools - /usr/local/bin/samtools [09:30:00] Found java - /usr/local/bin/java [09:30:00] Found snpEff - /usr/local/bin/snpEff [09:30:00] Found samclip - /usr/local/bin/samclip [09:30:00] Found seqtk - /usr/local/bin/seqtk [09:30:00] Found parallel - /usr/local/bin/parallel [09:30:00] Found freebayes - /usr/local/bin/freebayes [09:30:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [09:30:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [09:30:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [09:30:00] Found vcfuniq - /usr/local/bin/vcfuniq [09:30:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [09:30:00] Found gzip - /bin/gzip [09:30:00] Found vt - /usr/local/bin/vt [09:30:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [09:30:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [09:30:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [09:30:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [09:30:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [09:30:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [09:30:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [09:30:01] Using reference: /cvmfs/data.galaxyproject.org/byhand/Araly1/seq/Araly1.fa [09:30:02] Treating reference as 'fasta' format. [09:30:02] Will use 1 CPU cores. [09:30:02] Using read file: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat [09:30:02] Using read file: /corral4/main/objects/3/b/f/dataset_3bffcdc3-34b5-4333-9ca1-70773ed0ae26.dat [09:30:02] Creating folder: GCF_000195955_2_ASM19595v2_genomic_fna [09:30:02] Changing working directory: GCF_000195955_2_ASM19595v2_genomic_fna [09:30:02] Creating reference folder: reference [09:30:02] Extracting FASTA and GFF from reference. [09:30:10] Wrote 702 sequences to ref.fa [09:30:10] Wrote 0 features to ref.gff [09:30:10] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time. [09:30:10] Using BAM RG (Read Group) ID: GCF_000195955_2_ASM19595v2_genomic_fna [09:30:10] Running: samtools faidx reference/ref.fa 2>> snps.log [09:30:10] Error running command, check GCF_000195955_2_ASM19595v2_genomic_fna/snps.log
1[09:21:44] This is snippy 4.6.0
Show full stderr[09:21:44] This is snippy 4.6.0 [09:21:44] Written by Torsten Seemann [09:21:44] Obtained from https://github.com/tseemann/snippy [09:21:44] Detected operating system: linux [09:21:44] Enabling bundled linux tools. [09:21:44] Found bwa - /usr/local/bin/bwa [09:21:44] Found bcftools - /usr/local/bin/bcftools [09:21:44] Found samtools - /usr/local/bin/samtools [09:21:44] Found java - /usr/local/bin/java [09:21:44] Found snpEff - /usr/local/bin/snpEff [09:21:44] Found samclip - /usr/local/bin/samclip [09:21:44] Found seqtk - /usr/local/bin/seqtk [09:21:44] Found parallel - /usr/local/bin/parallel [09:21:44] Found freebayes - /usr/local/bin/freebayes [09:21:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [09:21:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [09:21:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [09:21:44] Found vcfuniq - /usr/local/bin/vcfuniq [09:21:44] Found vcffirstheader - /usr/local/bin/vcffirstheader [09:21:44] Found gzip - /bin/gzip [09:21:44] Found vt - /usr/local/bin/vt [09:21:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [09:21:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [09:21:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [09:21:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [09:21:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [09:21:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [09:21:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [09:21:44] Using reference: /cvmfs/data.galaxyproject.org/byhand/Araly1/seq/Araly1.fa [09:21:45] Treating reference as 'fasta' format. [09:21:45] Will use 1 CPU cores. [09:21:45] Using read file: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat [09:21:45] Using read file: /corral4/main/objects/6/b/1/dataset_6b1ad49a-4a2a-498d-8117-7497e94c0a80.dat [09:21:45] Creating folder: GCF_000195955_2_ASM19595v2_genomic_fna [09:21:45] Changing working directory: GCF_000195955_2_ASM19595v2_genomic_fna [09:21:45] Creating reference folder: reference [09:21:45] Extracting FASTA and GFF from reference. [09:21:53] Wrote 702 sequences to ref.fa [09:21:53] Wrote 0 features to ref.gff [09:21:53] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time. [09:21:53] Using BAM RG (Read Group) ID: GCF_000195955_2_ASM19595v2_genomic_fna [09:21:53] Running: samtools faidx reference/ref.fa 2>> snps.log [09:21:53] Error running command, check GCF_000195955_2_ASM19595v2_genomic_fna/snps.log
1[09:22:01] This is snippy 4.6.0
Show full stderr[09:22:01] This is snippy 4.6.0 [09:22:01] Written by Torsten Seemann [09:22:01] Obtained from https://github.com/tseemann/snippy [09:22:01] Detected operating system: linux [09:22:01] Enabling bundled linux tools. [09:22:01] Found bwa - /usr/local/bin/bwa [09:22:01] Found bcftools - /usr/local/bin/bcftools [09:22:01] Found samtools - /usr/local/bin/samtools [09:22:01] Found java - /usr/local/bin/java [09:22:01] Found snpEff - /usr/local/bin/snpEff [09:22:01] Found samclip - /usr/local/bin/samclip [09:22:01] Found seqtk - /usr/local/bin/seqtk [09:22:01] Found parallel - /usr/local/bin/parallel [09:22:01] Found freebayes - /usr/local/bin/freebayes [09:22:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [09:22:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [09:22:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [09:22:01] Found vcfuniq - /usr/local/bin/vcfuniq [09:22:01] Found vcffirstheader - /usr/local/bin/vcffirstheader [09:22:01] Found gzip - /bin/gzip [09:22:01] Found vt - /usr/local/bin/vt [09:22:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [09:22:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [09:22:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [09:22:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [09:22:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [09:22:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [09:22:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [09:22:01] Using reference: /cvmfs/data.galaxyproject.org/byhand/Araly1/seq/Araly1.fa [09:22:02] Treating reference as 'fasta' format. [09:22:02] Will use 1 CPU cores. [09:22:02] Using read file: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat [09:22:02] Using read file: /corral4/main/objects/e/3/8/dataset_e38132f1-37f3-4ab3-a022-cf955afaeefe.dat [09:22:02] Creating folder: GCF_000195955_2_ASM19595v2_genomic_fna [09:22:02] Changing working directory: GCF_000195955_2_ASM19595v2_genomic_fna [09:22:02] Creating reference folder: reference [09:22:02] Extracting FASTA and GFF from reference. [09:22:09] Wrote 702 sequences to ref.fa [09:22:09] Wrote 0 features to ref.gff [09:22:09] Freebayes will process 1 chunks of 210374351 bp, 1 chunks at a time. [09:22:09] Using BAM RG (Read Group) ID: GCF_000195955_2_ASM19595v2_genomic_fna [09:22:09] Running: samtools faidx reference/ref.fa 2>> snps.log [09:22:10] Running: bwa index reference/ref.fa 2>> snps.log [09:25:17] Error running command, check GCF_000195955_2_ASM19595v2_genomic_fna/snps.log
1[09:22:07] This is snippy 4.6.0
Show full stderr[09:22:07] This is snippy 4.6.0 [09:22:07] Written by Torsten Seemann [09:22:07] Obtained from https://github.com/tseemann/snippy [09:22:07] Detected operating system: linux [09:22:07] Enabling bundled linux tools. [09:22:07] Found bwa - /usr/local/bin/bwa [09:22:07] Found bcftools - /usr/local/bin/bcftools [09:22:07] Found samtools - /usr/local/bin/samtools [09:22:07] Found java - /usr/local/bin/java [09:22:07] Found snpEff - /usr/local/bin/snpEff [09:22:07] Found samclip - /usr/local/bin/samclip [09:22:07] Found seqtk - /usr/local/bin/seqtk [09:22:07] Found parallel - /usr/local/bin/parallel [09:22:07] Found freebayes - /usr/local/bin/freebayes [09:22:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [09:22:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [09:22:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [09:22:07] Found vcfuniq - /usr/local/bin/vcfuniq [09:22:07] Found vcffirstheader - /usr/local/bin/vcffirstheader [09:22:07] Found gzip - /bin/gzip [09:22:07] Found vt - /usr/local/bin/vt [09:22:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [09:22:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [09:22:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [09:22:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [09:22:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [09:22:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [09:22:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [09:22:08] Using reference: /cvmfs/data.galaxyproject.org/byhand/Araly1/seq/Araly1.fa [09:22:08] Treating reference as 'fasta' format. [09:22:08] Will use 1 CPU cores. [09:22:08] Using read file: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat [09:22:08] Using read file: /corral4/main/objects/e/3/0/dataset_e3005d69-11fb-4397-84d6-fdd8617a4c65.dat [09:22:08] Creating folder: GCF_000195955_2_ASM19595v2_genomic_fna [09:22:08] Changing working directory: GCF_000195955_2_ASM19595v2_genomic_fna [09:22:08] Creating reference folder: reference [09:22:08] Extracting FASTA and GFF from reference. [09:22:16] Wrote 702 sequences to ref.fa [09:22:16] Wrote 0 features to ref.gff [09:22:16] Freebayes will process 1 chunks of 210374351 bp, 1 chunks at a time. [09:22:16] Using BAM RG (Read Group) ID: GCF_000195955_2_ASM19595v2_genomic_fna [09:22:16] Running: samtools faidx reference/ref.fa 2>> snps.log [09:22:17] Running: bwa index reference/ref.fa 2>> snps.log [09:25:28] Error running command, check GCF_000195955_2_ASM19595v2_genomic_fna/snps.log
1[09:25:32] This is snippy 4.6.0
Show full stderr[09:25:32] This is snippy 4.6.0 [09:25:32] Written by Torsten Seemann [09:25:32] Obtained from https://github.com/tseemann/snippy [09:25:32] Detected operating system: linux [09:25:32] Enabling bundled linux tools. [09:25:32] Found bwa - /usr/local/bin/bwa [09:25:32] Found bcftools - /usr/local/bin/bcftools [09:25:32] Found samtools - /usr/local/bin/samtools [09:25:32] Found java - /usr/local/bin/java [09:25:32] Found snpEff - /usr/local/bin/snpEff [09:25:32] Found samclip - /usr/local/bin/samclip [09:25:32] Found seqtk - /usr/local/bin/seqtk [09:25:32] Found parallel - /usr/local/bin/parallel [09:25:32] Found freebayes - /usr/local/bin/freebayes [09:25:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [09:25:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [09:25:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [09:25:33] Found vcfuniq - /usr/local/bin/vcfuniq [09:25:33] Found vcffirstheader - /usr/local/bin/vcffirstheader [09:25:33] Found gzip - /bin/gzip [09:25:33] Found vt - /usr/local/bin/vt [09:25:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [09:25:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [09:25:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [09:25:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [09:25:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [09:25:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [09:25:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [09:25:33] Using reference: /cvmfs/data.galaxyproject.org/byhand/Araly1/seq/Araly1.fa [09:25:34] Treating reference as 'fasta' format. [09:25:34] Will use 1 CPU cores. [09:25:34] Using read file: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat [09:25:34] Using read file: /corral4/main/objects/7/f/4/dataset_7f4fdad8-5c88-45d2-be21-9de2a47232a3.dat [09:25:34] Creating folder: GCF_000195955_2_ASM19595v2_genomic_fna [09:25:34] Changing working directory: GCF_000195955_2_ASM19595v2_genomic_fna [09:25:34] Creating reference folder: reference [09:25:34] Extracting FASTA and GFF from reference. [09:25:41] Wrote 702 sequences to ref.fa [09:25:41] Wrote 0 features to ref.gff [09:25:42] Freebayes will process 1 chunks of 210374351 bp, 1 chunks at a time. [09:25:42] Using BAM RG (Read Group) ID: GCF_000195955_2_ASM19595v2_genomic_fna [09:25:42] Running: samtools faidx reference/ref.fa 2>> snps.log [09:25:43] Running: bwa index reference/ref.fa 2>> snps.log [09:28:52] Error running command, check GCF_000195955_2_ASM19595v2_genomic_fna/snps.log
1[09:25:43] This is snippy 4.6.0
Show full stderr[09:25:43] This is snippy 4.6.0 [09:25:43] Written by Torsten Seemann [09:25:43] Obtained from https://github.com/tseemann/snippy [09:25:43] Detected operating system: linux [09:25:43] Enabling bundled linux tools. [09:25:43] Found bwa - /usr/local/bin/bwa [09:25:43] Found bcftools - /usr/local/bin/bcftools [09:25:43] Found samtools - /usr/local/bin/samtools [09:25:43] Found java - /usr/local/bin/java [09:25:43] Found snpEff - /usr/local/bin/snpEff [09:25:43] Found samclip - /usr/local/bin/samclip [09:25:43] Found seqtk - /usr/local/bin/seqtk [09:25:43] Found parallel - /usr/local/bin/parallel [09:25:43] Found freebayes - /usr/local/bin/freebayes [09:25:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [09:25:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [09:25:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [09:25:43] Found vcfuniq - /usr/local/bin/vcfuniq [09:25:43] Found vcffirstheader - /usr/local/bin/vcffirstheader [09:25:43] Found gzip - /bin/gzip [09:25:43] Found vt - /usr/local/bin/vt [09:25:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [09:25:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [09:25:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [09:25:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [09:25:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [09:25:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [09:25:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [09:25:44] Using reference: /cvmfs/data.galaxyproject.org/byhand/Araly1/seq/Araly1.fa [09:25:44] Treating reference as 'fasta' format. [09:25:44] Will use 1 CPU cores. [09:25:44] Using read file: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat [09:25:44] Using read file: /corral4/main/objects/4/f/a/dataset_4faba0fc-8fba-4a16-8711-0dcecfb7bd3a.dat [09:25:44] Creating folder: GCF_000195955_2_ASM19595v2_genomic_fna [09:25:44] Changing working directory: GCF_000195955_2_ASM19595v2_genomic_fna [09:25:44] Creating reference folder: reference [09:25:44] Extracting FASTA and GFF from reference. [09:25:52] Wrote 702 sequences to ref.fa [09:25:52] Wrote 0 features to ref.gff [09:25:52] Freebayes will process 1 chunks of 210374351 bp, 1 chunks at a time. [09:25:52] Using BAM RG (Read Group) ID: GCF_000195955_2_ASM19595v2_genomic_fna [09:25:52] Running: samtools faidx reference/ref.fa 2>> snps.log [09:25:52] Error running command, check GCF_000195955_2_ASM19595v2_genomic_fna/snps.log
1[09:21:38] This is snippy 4.6.0
Show full stderr[09:21:38] This is snippy 4.6.0 [09:21:38] Written by Torsten Seemann [09:21:38] Obtained from https://github.com/tseemann/snippy [09:21:38] Detected operating system: linux [09:21:38] Enabling bundled linux tools. [09:21:38] Found bwa - /usr/local/bin/bwa [09:21:38] Found bcftools - /usr/local/bin/bcftools [09:21:38] Found samtools - /usr/local/bin/samtools [09:21:38] Found java - /usr/local/bin/java [09:21:38] Found snpEff - /usr/local/bin/snpEff [09:21:38] Found samclip - /usr/local/bin/samclip [09:21:38] Found seqtk - /usr/local/bin/seqtk [09:21:38] Found parallel - /usr/local/bin/parallel [09:21:38] Found freebayes - /usr/local/bin/freebayes [09:21:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [09:21:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [09:21:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [09:21:38] Found vcfuniq - /usr/local/bin/vcfuniq [09:21:38] Found vcffirstheader - /usr/local/bin/vcffirstheader [09:21:38] Found gzip - /bin/gzip [09:21:38] Found vt - /usr/local/bin/vt [09:21:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [09:21:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [09:21:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [09:21:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [09:21:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [09:21:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [09:21:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [09:21:38] Using reference: /cvmfs/data.galaxyproject.org/byhand/Araly1/seq/Araly1.fa [09:21:39] Treating reference as 'fasta' format. [09:21:39] Will use 1 CPU cores. [09:21:39] Using read file: /corral4/main/objects/0/b/7/dataset_0b7a93af-75e8-4a47-9db8-24cd408e15b8.dat [09:21:39] Using read file: /corral4/main/objects/2/4/f/dataset_24f9e80a-5c47-4236-865c-7d075421adfd.dat [09:21:39] Creating folder: GCF_000195955_2_ASM19595v2_genomic_fna [09:21:39] Changing working directory: GCF_000195955_2_ASM19595v2_genomic_fna [09:21:39] Creating reference folder: reference [09:21:39] Extracting FASTA and GFF from reference. [09:21:46] Wrote 702 sequences to ref.fa [09:21:46] Wrote 0 features to ref.gff [09:21:47] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time. [09:21:47] Using BAM RG (Read Group) ID: GCF_000195955_2_ASM19595v2_genomic_fna [09:21:47] Running: samtools faidx reference/ref.fa 2>> snps.log [09:21:47] Error running command, check GCF_000195955_2_ASM19595v2_genomic_fna/snps.log
1[13:07:15] This is snippy 4.6.0
Show full stderr[13:07:15] This is snippy 4.6.0 [13:07:15] Written by Torsten Seemann [13:07:15] Obtained from https://github.com/tseemann/snippy [13:07:15] Detected operating system: linux [13:07:15] Enabling bundled linux tools. [13:07:15] Found bwa - /usr/local/bin/bwa [13:07:15] Found bcftools - /usr/local/bin/bcftools [13:07:15] Found samtools - /usr/local/bin/samtools [13:07:15] Found java - /usr/local/bin/java [13:07:15] Found snpEff - /usr/local/bin/snpEff [13:07:15] Found samclip - /usr/local/bin/samclip [13:07:15] Found seqtk - /usr/local/bin/seqtk [13:07:15] Found parallel - /usr/local/bin/parallel [13:07:15] Found freebayes - /usr/local/bin/freebayes [13:07:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [13:07:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [13:07:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [13:07:15] Found vcfuniq - /usr/local/bin/vcfuniq [13:07:15] Found vcffirstheader - /usr/local/bin/vcffirstheader [13:07:15] Found gzip - /bin/gzip [13:07:15] Found vt - /usr/local/bin/vt [13:07:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [13:07:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [13:07:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [13:07:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [13:07:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [13:07:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [13:07:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [13:07:15] Using reference: /jetstream2/scratch/main/jobs/72274628/inputs/dataset_8c4a0e80-4ef9-43df-add5-2cfde861170d.dat [13:07:15] Treating reference as 'fasta' format. [13:07:15] Will use 1 CPU cores. [13:07:15] Using read file: /jetstream2/scratch/main/jobs/72274628/inputs/dataset_528cab5d-bce5-4533-80c7-807895d7ede6.dat [13:07:15] Creating folder: Select_on_dataset_10 [13:07:15] Changing working directory: Select_on_dataset_10 [13:07:15] Creating reference folder: reference [13:07:15] Extracting FASTA and GFF from reference. [13:07:16] Wrote 3 sequences to ref.fa [13:07:16] Wrote 0 features to ref.gff [13:07:16] Freebayes will process 1 chunks of 9205924 bp, 1 chunks at a time. [13:07:16] Using BAM RG (Read Group) ID: Select_on_dataset_10 [13:07:16] Running: samtools faidx reference/ref.fa 2>> snps.log [13:07:16] Running: bwa index reference/ref.fa 2>> snps.log [13:07:19] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [13:07:19] Running: ln -sf reference/ref.fa . 2>> snps.log [13:07:19] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [13:07:19] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [13:07:19] Running: bwa mem -Y -M -R '@RG\tID:Select_on_dataset_10\tSM:Select_on_dataset_10' -t 1 reference/ref.fa /jetstream2/scratch/main/jobs/72274628/inputs/dataset_528cab5d-bce5-4533-80c7-807895d7ede6.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/72274628/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/72274628/tmp --threads 0 -m 12000M | samtools markdup -T /jetstream2/scratch/main/jobs/72274628/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 3 sequences in reference/ref.fa.fai [M::process] read 1 sequences (10262635 bp)... [M::mem_process_seqs] Processed
1[13:17:39] This is snippy 4.6.0
Show full stderr[13:17:39] This is snippy 4.6.0 [13:17:39] Written by Torsten Seemann [13:17:39] Obtained from https://github.com/tseemann/snippy [13:17:39] Detected operating system: linux [13:17:39] Enabling bundled linux tools. [13:17:39] Found bwa - /usr/local/bin/bwa [13:17:39] Found bcftools - /usr/local/bin/bcftools [13:17:39] Found samtools - /usr/local/bin/samtools [13:17:39] Found java - /usr/local/bin/java [13:17:39] Found snpEff - /usr/local/bin/snpEff [13:17:39] Found samclip - /usr/local/bin/samclip [13:17:39] Found seqtk - /usr/local/bin/seqtk [13:17:39] Found parallel - /usr/local/bin/parallel [13:17:39] Found freebayes - /usr/local/bin/freebayes [13:17:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [13:17:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [13:17:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [13:17:39] Found vcfuniq - /usr/local/bin/vcfuniq [13:17:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [13:17:39] Found gzip - /bin/gzip [13:17:39] Found vt - /usr/local/bin/vt [13:17:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [13:17:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [13:17:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [13:17:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [13:17:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [13:17:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [13:17:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [13:17:39] Using reference: /jetstream2/scratch/main/jobs/72274648/inputs/dataset_8c4a0e80-4ef9-43df-add5-2cfde861170d.dat [13:17:39] Treating reference as 'fasta' format. [13:17:39] Will use 1 CPU cores. [13:17:39] Using read file: /jetstream2/scratch/main/jobs/72274648/inputs/dataset_2fc7b817-f05e-4fd8-bc46-5fee29524df4.dat [13:17:39] Creating folder: Select_on_dataset_1 [13:17:39] Changing working directory: Select_on_dataset_1 [13:17:39] Creating reference folder: reference [13:17:39] Extracting FASTA and GFF from reference. [13:17:40] Wrote 3 sequences to ref.fa [13:17:40] Wrote 0 features to ref.gff [13:17:40] Freebayes will process 1 chunks of 9205924 bp, 1 chunks at a time. [13:17:40] Using BAM RG (Read Group) ID: Select_on_dataset_1 [13:17:40] Running: samtools faidx reference/ref.fa 2>> snps.log [13:17:40] Running: bwa index reference/ref.fa 2>> snps.log [13:17:43] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [13:17:43] Running: ln -sf reference/ref.fa . 2>> snps.log [13:17:43] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [13:17:43] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [13:17:43] Running: bwa mem -Y -M -R '@RG\tID:Select_on_dataset_1\tSM:Select_on_dataset_1' -t 1 reference/ref.fa /jetstream2/scratch/main/jobs/72274648/inputs/dataset_2fc7b817-f05e-4fd8-bc46-5fee29524df4.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/72274648/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/72274648/tmp --threads 0 -m 12000M | samtools markdup -T /jetstream2/scratch/main/jobs/72274648/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 3 sequences in reference/ref.fa.fai [M::process] read 2 sequences (9782257 bp)... [M::mem_process_seqs] Processed 2 rea
1[14:38:58] This is snippy 4.6.0
Show full stderr[14:38:58] This is snippy 4.6.0 [14:38:58] Written by Torsten Seemann [14:38:58] Obtained from https://github.com/tseemann/snippy [14:38:58] Detected operating system: linux [14:38:58] Enabling bundled linux tools. [14:38:58] Found bwa - /usr/local/bin/bwa [14:38:58] Found bcftools - /usr/local/bin/bcftools [14:38:58] Found samtools - /usr/local/bin/samtools [14:38:58] Found java - /usr/local/bin/java [14:38:58] Found snpEff - /usr/local/bin/snpEff [14:38:58] Found samclip - /usr/local/bin/samclip [14:38:58] Found seqtk - /usr/local/bin/seqtk [14:38:58] Found parallel - /usr/local/bin/parallel [14:38:58] Found freebayes - /usr/local/bin/freebayes [14:38:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:38:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:38:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:38:58] Found vcfuniq - /usr/local/bin/vcfuniq [14:38:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:38:58] Found gzip - /bin/gzip [14:38:58] Found vt - /usr/local/bin/vt [14:38:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:38:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:38:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:38:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:38:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:38:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:38:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:38:58] Using reference: /jetstream2/scratch/main/jobs/72276988/inputs/dataset_8c4a0e80-4ef9-43df-add5-2cfde861170d.dat [14:38:59] Treating reference as 'fasta' format. [14:38:59] Will use 1 CPU cores. [14:38:59] Using read file: /jetstream2/scratch/main/jobs/72276988/inputs/dataset_528cab5d-bce5-4533-80c7-807895d7ede6.dat [14:38:59] Creating folder: Select_on_dataset_10 [14:38:59] Changing working directory: Select_on_dataset_10 [14:38:59] Creating reference folder: reference [14:38:59] Extracting FASTA and GFF from reference. [14:38:59] Wrote 3 sequences to ref.fa [14:38:59] Wrote 0 features to ref.gff [14:38:59] Freebayes will process 1 chunks of 9205924 bp, 1 chunks at a time. [14:38:59] Using BAM RG (Read Group) ID: Select_on_dataset_10 [14:38:59] Running: samtools faidx reference/ref.fa 2>> snps.log [14:38:59] Running: bwa index reference/ref.fa 2>> snps.log [14:39:02] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [14:39:02] Running: ln -sf reference/ref.fa . 2>> snps.log [14:39:02] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [14:39:02] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [14:39:02] Running: bwa mem -Y -M -R '@RG\tID:Select_on_dataset_10\tSM:Select_on_dataset_10' -t 1 reference/ref.fa /jetstream2/scratch/main/jobs/72276988/inputs/dataset_528cab5d-bce5-4533-80c7-807895d7ede6.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/72276988/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/72276988/tmp --threads 0 -m 12000M | samtools markdup -T /jetstream2/scratch/main/jobs/72276988/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 3 sequences in reference/ref.fa.fai [M::process] read 1 sequences (10262635 bp)... [M::mem_process_seqs] Processed
1[14:43:57] This is snippy 4.6.0
Show full stderr[14:43:57] This is snippy 4.6.0 [14:43:57] Written by Torsten Seemann [14:43:57] Obtained from https://github.com/tseemann/snippy [14:43:57] Detected operating system: linux [14:43:57] Enabling bundled linux tools. [14:43:57] Found bwa - /usr/local/bin/bwa [14:43:57] Found bcftools - /usr/local/bin/bcftools [14:43:57] Found samtools - /usr/local/bin/samtools [14:43:57] Found java - /usr/local/bin/java [14:43:57] Found snpEff - /usr/local/bin/snpEff [14:43:57] Found samclip - /usr/local/bin/samclip [14:43:57] Found seqtk - /usr/local/bin/seqtk [14:43:57] Found parallel - /usr/local/bin/parallel [14:43:57] Found freebayes - /usr/local/bin/freebayes [14:43:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:43:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:43:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:43:57] Found vcfuniq - /usr/local/bin/vcfuniq [14:43:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:43:57] Found gzip - /bin/gzip [14:43:57] Found vt - /usr/local/bin/vt [14:43:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:43:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:43:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:43:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:43:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:43:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:43:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:43:58] Using reference: /jetstream2/scratch/main/jobs/72276992/inputs/dataset_8c4a0e80-4ef9-43df-add5-2cfde861170d.dat [14:43:58] Treating reference as 'fasta' format. [14:43:58] Will use 1 CPU cores. [14:43:58] Using read file: /jetstream2/scratch/main/jobs/72276992/inputs/dataset_721aefd6-f7c7-4a1b-96ab-de8d3a958004.dat [14:43:58] Creating folder: Select_on_dataset_15 [14:43:58] Changing working directory: Select_on_dataset_15 [14:43:58] Creating reference folder: reference [14:43:58] Extracting FASTA and GFF from reference. [14:43:59] Wrote 3 sequences to ref.fa [14:43:59] Wrote 0 features to ref.gff [14:43:59] Freebayes will process 1 chunks of 9205924 bp, 1 chunks at a time. [14:43:59] Using BAM RG (Read Group) ID: Select_on_dataset_15 [14:43:59] Running: samtools faidx reference/ref.fa 2>> snps.log [14:43:59] Running: bwa index reference/ref.fa 2>> snps.log [14:44:02] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [14:44:02] Running: ln -sf reference/ref.fa . 2>> snps.log [14:44:02] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [14:44:02] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [14:44:02] Running: bwa mem -Y -M -R '@RG\tID:Select_on_dataset_15\tSM:Select_on_dataset_15' -t 1 reference/ref.fa /jetstream2/scratch/main/jobs/72276992/inputs/dataset_721aefd6-f7c7-4a1b-96ab-de8d3a958004.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/72276992/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/72276992/tmp --threads 0 -m 12000M | samtools markdup -T /jetstream2/scratch/main/jobs/72276992/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 3 sequences in reference/ref.fa.fai [M::process] read 1 sequences (10101518 bp)... [M::mem_process_seqs] Processed
1[14:46:53] This is snippy 4.6.0
Show full stderr[14:46:53] This is snippy 4.6.0 [14:46:53] Written by Torsten Seemann [14:46:53] Obtained from https://github.com/tseemann/snippy [14:46:53] Detected operating system: linux [14:46:53] Enabling bundled linux tools. [14:46:53] Found bwa - /usr/local/bin/bwa [14:46:53] Found bcftools - /usr/local/bin/bcftools [14:46:53] Found samtools - /usr/local/bin/samtools [14:46:53] Found java - /usr/local/bin/java [14:46:53] Found snpEff - /usr/local/bin/snpEff [14:46:53] Found samclip - /usr/local/bin/samclip [14:46:53] Found seqtk - /usr/local/bin/seqtk [14:46:53] Found parallel - /usr/local/bin/parallel [14:46:53] Found freebayes - /usr/local/bin/freebayes [14:46:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:46:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:46:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:46:53] Found vcfuniq - /usr/local/bin/vcfuniq [14:46:53] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:46:53] Found gzip - /bin/gzip [14:46:53] Found vt - /usr/local/bin/vt [14:46:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:46:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:46:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:46:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:46:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:46:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:46:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:46:54] Using reference: /jetstream2/scratch/main/jobs/72276995/inputs/dataset_8c4a0e80-4ef9-43df-add5-2cfde861170d.dat [14:46:54] Treating reference as 'fasta' format. [14:46:54] Will use 1 CPU cores. [14:46:54] Using read file: /jetstream2/scratch/main/jobs/72276995/inputs/dataset_20845546-a649-4a94-aa76-3444d7ff9ff5.dat [14:46:54] Creating folder: Select_on_dataset_18 [14:46:54] Changing working directory: Select_on_dataset_18 [14:46:54] Creating reference folder: reference [14:46:54] Extracting FASTA and GFF from reference. [14:46:55] Wrote 3 sequences to ref.fa [14:46:55] Wrote 0 features to ref.gff [14:46:55] Freebayes will process 1 chunks of 9205924 bp, 1 chunks at a time. [14:46:55] Using BAM RG (Read Group) ID: Select_on_dataset_18 [14:46:55] Running: samtools faidx reference/ref.fa 2>> snps.log [14:46:55] Running: bwa index reference/ref.fa 2>> snps.log [14:46:58] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [14:46:59] Running: ln -sf reference/ref.fa . 2>> snps.log [14:46:59] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [14:46:59] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [14:46:59] Running: bwa mem -Y -M -R '@RG\tID:Select_on_dataset_18\tSM:Select_on_dataset_18' -t 1 reference/ref.fa /jetstream2/scratch/main/jobs/72276995/inputs/dataset_20845546-a649-4a94-aa76-3444d7ff9ff5.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/72276995/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/72276995/tmp --threads 0 -m 12000M | samtools markdup -T /jetstream2/scratch/main/jobs/72276995/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 3 sequences in reference/ref.fa.fai [M::process] read 3 sequences (9598041 bp)... [M::mem_process_seqs] Processed 3
1[14:36:13] This is snippy 4.6.0
Show full stderr[14:36:13] This is snippy 4.6.0 [14:36:13] Written by Torsten Seemann [14:36:13] Obtained from https://github.com/tseemann/snippy [14:36:13] Detected operating system: linux [14:36:13] Enabling bundled linux tools. [14:36:14] Found bwa - /usr/local/bin/bwa [14:36:14] Found bcftools - /usr/local/bin/bcftools [14:36:14] Found samtools - /usr/local/bin/samtools [14:36:14] Found java - /usr/local/bin/java [14:36:14] Found snpEff - /usr/local/bin/snpEff [14:36:14] Found samclip - /usr/local/bin/samclip [14:36:14] Found seqtk - /usr/local/bin/seqtk [14:36:14] Found parallel - /usr/local/bin/parallel [14:36:14] Found freebayes - /usr/local/bin/freebayes [14:36:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:36:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:36:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:36:14] Found vcfuniq - /usr/local/bin/vcfuniq [14:36:14] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:36:14] Found gzip - /bin/gzip [14:36:14] Found vt - /usr/local/bin/vt [14:36:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:36:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:36:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:36:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:36:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:36:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:36:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:36:14] Using reference: /jetstream2/scratch/main/jobs/72277004/inputs/dataset_8c4a0e80-4ef9-43df-add5-2cfde861170d.dat [14:36:14] Treating reference as 'fasta' format. [14:36:14] Will use 1 CPU cores. [14:36:14] Using read file: /jetstream2/scratch/main/jobs/72277004/inputs/dataset_88444cf6-27f7-44aa-93a7-00a38bdbf1f8.dat [14:36:14] Creating folder: Select_on_dataset_28 [14:36:14] Changing working directory: Select_on_dataset_28 [14:36:14] Creating reference folder: reference [14:36:14] Extracting FASTA and GFF from reference. [14:36:15] Wrote 3 sequences to ref.fa [14:36:15] Wrote 0 features to ref.gff [14:36:15] Freebayes will process 1 chunks of 9205924 bp, 1 chunks at a time. [14:36:15] Using BAM RG (Read Group) ID: Select_on_dataset_28 [14:36:15] Running: samtools faidx reference/ref.fa 2>> snps.log [14:36:15] Running: bwa index reference/ref.fa 2>> snps.log [14:36:18] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [14:36:18] Running: ln -sf reference/ref.fa . 2>> snps.log [14:36:18] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [14:36:18] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [14:36:18] Running: bwa mem -Y -M -R '@RG\tID:Select_on_dataset_28\tSM:Select_on_dataset_28' -t 1 reference/ref.fa /jetstream2/scratch/main/jobs/72277004/inputs/dataset_88444cf6-27f7-44aa-93a7-00a38bdbf1f8.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/72277004/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/72277004/tmp --threads 0 -m 12000M | samtools markdup -T /jetstream2/scratch/main/jobs/72277004/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 3 sequences in reference/ref.fa.fai [M::process] read 1 sequences (12213033 bp)... [M::mem_process_seqs] Processed
1[17:50:23] This is snippy 4.6.0
Show full stderr[17:50:23] This is snippy 4.6.0 [17:50:23] Written by Torsten Seemann [17:50:23] Obtained from https://github.com/tseemann/snippy [17:50:23] Detected operating system: linux [17:50:23] Enabling bundled linux tools. [17:50:23] Found bwa - /usr/local/bin/bwa [17:50:23] Found bcftools - /usr/local/bin/bcftools [17:50:23] Found samtools - /usr/local/bin/samtools [17:50:23] Found java - /usr/local/bin/java [17:50:23] Found snpEff - /usr/local/bin/snpEff [17:50:23] Found samclip - /usr/local/bin/samclip [17:50:23] Found seqtk - /usr/local/bin/seqtk [17:50:23] Found parallel - /usr/local/bin/parallel [17:50:23] Found freebayes - /usr/local/bin/freebayes [17:50:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:50:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:50:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:50:23] Found vcfuniq - /usr/local/bin/vcfuniq [17:50:23] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:50:23] Found gzip - /bin/gzip [17:50:23] Found vt - /usr/local/bin/vt [17:50:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:50:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:50:23] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:50:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:50:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:50:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:50:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:50:24] Using reference: /jetstream2/scratch/main/jobs/72283434/inputs/dataset_8c4a0e80-4ef9-43df-add5-2cfde861170d.dat [17:50:24] Treating reference as 'fasta' format. [17:50:24] Will use 1 CPU cores. [17:50:24] Using read file: /jetstream2/scratch/main/jobs/72283434/inputs/dataset_20845546-a649-4a94-aa76-3444d7ff9ff5.dat [17:50:24] Creating folder: Select_on_dataset_18 [17:50:24] Changing working directory: Select_on_dataset_18 [17:50:24] Creating reference folder: reference [17:50:24] Extracting FASTA and GFF from reference. [17:50:25] Wrote 3 sequences to ref.fa [17:50:25] Wrote 0 features to ref.gff [17:50:25] Freebayes will process 1 chunks of 9205924 bp, 1 chunks at a time. [17:50:25] Using BAM RG (Read Group) ID: Select_on_dataset_18 [17:50:25] Running: samtools faidx reference/ref.fa 2>> snps.log [17:50:25] Running: bwa index reference/ref.fa 2>> snps.log [17:50:28] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [17:50:29] Running: ln -sf reference/ref.fa . 2>> snps.log [17:50:29] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [17:50:29] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [17:50:29] Running: bwa mem -Y -M -R '@RG\tID:Select_on_dataset_18\tSM:Select_on_dataset_18' -t 1 reference/ref.fa /jetstream2/scratch/main/jobs/72283434/inputs/dataset_20845546-a649-4a94-aa76-3444d7ff9ff5.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/72283434/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/72283434/tmp --threads 0 -m 12000M | samtools markdup -T /jetstream2/scratch/main/jobs/72283434/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 3 sequences in reference/ref.fa.fai [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::process] read 3 sequences (9598041 bp)... [M::mem_process_seqs] Processed 3
1[19:30:05] This is snippy 4.6.0
Show full stderr[19:30:05] This is snippy 4.6.0 [19:30:05] Written by Torsten Seemann [19:30:05] Obtained from https://github.com/tseemann/snippy [19:30:05] Detected operating system: linux [19:30:05] Enabling bundled linux tools. [19:30:05] Found bwa - /usr/local/bin/bwa [19:30:05] Found bcftools - /usr/local/bin/bcftools [19:30:05] Found samtools - /usr/local/bin/samtools [19:30:05] Found java - /usr/local/bin/java [19:30:05] Found snpEff - /usr/local/bin/snpEff [19:30:05] Found samclip - /usr/local/bin/samclip [19:30:05] Found seqtk - /usr/local/bin/seqtk [19:30:05] Found parallel - /usr/local/bin/parallel [19:30:05] Found freebayes - /usr/local/bin/freebayes [19:30:05] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [19:30:05] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [19:30:05] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [19:30:05] Found vcfuniq - /usr/local/bin/vcfuniq [19:30:05] Found vcffirstheader - /usr/local/bin/vcffirstheader [19:30:05] Found gzip - /bin/gzip [19:30:05] Found vt - /usr/local/bin/vt [19:30:05] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [19:30:05] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [19:30:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [19:30:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [19:30:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [19:30:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [19:30:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [19:30:06] Using reference: /corral4/main/objects/d/2/b/dataset_d2be515a-eac5-47a6-9e5f-c856da7a145f.dat [19:30:06] Could not guess format '/corral4/main/objects/d/2/b/dataset_d2be515a-eac5-47a6-9e5f-c856da7a145f.dat'
1[04:43:25] This is snippy 4.6.0
Show full stderr[04:43:25] This is snippy 4.6.0 [04:43:25] Written by Torsten Seemann [04:43:25] Obtained from https://github.com/tseemann/snippy [04:43:25] Detected operating system: linux [04:43:25] Enabling bundled linux tools. [04:43:25] Found bwa - /usr/local/bin/bwa [04:43:25] Found bcftools - /usr/local/bin/bcftools [04:43:25] Found samtools - /usr/local/bin/samtools [04:43:25] Found java - /usr/local/bin/java [04:43:25] Found snpEff - /usr/local/bin/snpEff [04:43:25] Found samclip - /usr/local/bin/samclip [04:43:25] Found seqtk - /usr/local/bin/seqtk [04:43:25] Found parallel - /usr/local/bin/parallel [04:43:25] Found freebayes - /usr/local/bin/freebayes [04:43:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:43:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:43:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:43:25] Found vcfuniq - /usr/local/bin/vcfuniq [04:43:25] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:43:25] Found gzip - /bin/gzip [04:43:25] Found vt - /usr/local/bin/vt [04:43:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:43:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:43:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:43:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:43:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:43:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:43:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:43:26] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:43:45] This is snippy 4.6.0
Show full stderr[04:43:45] This is snippy 4.6.0 [04:43:45] Written by Torsten Seemann [04:43:45] Obtained from https://github.com/tseemann/snippy [04:43:45] Detected operating system: linux [04:43:45] Enabling bundled linux tools. [04:43:45] Found bwa - /usr/local/bin/bwa [04:43:45] Found bcftools - /usr/local/bin/bcftools [04:43:45] Found samtools - /usr/local/bin/samtools [04:43:45] Found java - /usr/local/bin/java [04:43:45] Found snpEff - /usr/local/bin/snpEff [04:43:45] Found samclip - /usr/local/bin/samclip [04:43:45] Found seqtk - /usr/local/bin/seqtk [04:43:45] Found parallel - /usr/local/bin/parallel [04:43:45] Found freebayes - /usr/local/bin/freebayes [04:43:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:43:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:43:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:43:45] Found vcfuniq - /usr/local/bin/vcfuniq [04:43:45] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:43:45] Found gzip - /bin/gzip [04:43:45] Found vt - /usr/local/bin/vt [04:43:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:43:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:43:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:43:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:43:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:43:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:43:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:43:46] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:43:36] This is snippy 4.6.0
Show full stderr[04:43:36] This is snippy 4.6.0 [04:43:36] Written by Torsten Seemann [04:43:36] Obtained from https://github.com/tseemann/snippy [04:43:36] Detected operating system: linux [04:43:36] Enabling bundled linux tools. [04:43:36] Found bwa - /usr/local/bin/bwa [04:43:36] Found bcftools - /usr/local/bin/bcftools [04:43:36] Found samtools - /usr/local/bin/samtools [04:43:36] Found java - /usr/local/bin/java [04:43:37] Found snpEff - /usr/local/bin/snpEff [04:43:37] Found samclip - /usr/local/bin/samclip [04:43:37] Found seqtk - /usr/local/bin/seqtk [04:43:37] Found parallel - /usr/local/bin/parallel [04:43:37] Found freebayes - /usr/local/bin/freebayes [04:43:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:43:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:43:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:43:37] Found vcfuniq - /usr/local/bin/vcfuniq [04:43:37] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:43:37] Found gzip - /bin/gzip [04:43:37] Found vt - /usr/local/bin/vt [04:43:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:43:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:43:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:43:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:43:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:43:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:43:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:43:37] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:43:39] This is snippy 4.6.0
Show full stderr[04:43:39] This is snippy 4.6.0 [04:43:39] Written by Torsten Seemann [04:43:39] Obtained from https://github.com/tseemann/snippy [04:43:39] Detected operating system: linux [04:43:39] Enabling bundled linux tools. [04:43:39] Found bwa - /usr/local/bin/bwa [04:43:39] Found bcftools - /usr/local/bin/bcftools [04:43:39] Found samtools - /usr/local/bin/samtools [04:43:39] Found java - /usr/local/bin/java [04:43:39] Found snpEff - /usr/local/bin/snpEff [04:43:39] Found samclip - /usr/local/bin/samclip [04:43:39] Found seqtk - /usr/local/bin/seqtk [04:43:39] Found parallel - /usr/local/bin/parallel [04:43:39] Found freebayes - /usr/local/bin/freebayes [04:43:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:43:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:43:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:43:39] Found vcfuniq - /usr/local/bin/vcfuniq [04:43:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:43:39] Found gzip - /bin/gzip [04:43:39] Found vt - /usr/local/bin/vt [04:43:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:43:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:43:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:43:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:43:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:43:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:43:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:43:40] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:43:43] This is snippy 4.6.0
Show full stderr[04:43:43] This is snippy 4.6.0 [04:43:43] Written by Torsten Seemann [04:43:43] Obtained from https://github.com/tseemann/snippy [04:43:43] Detected operating system: linux [04:43:43] Enabling bundled linux tools. [04:43:43] Found bwa - /usr/local/bin/bwa [04:43:43] Found bcftools - /usr/local/bin/bcftools [04:43:43] Found samtools - /usr/local/bin/samtools [04:43:43] Found java - /usr/local/bin/java [04:43:43] Found snpEff - /usr/local/bin/snpEff [04:43:43] Found samclip - /usr/local/bin/samclip [04:43:43] Found seqtk - /usr/local/bin/seqtk [04:43:43] Found parallel - /usr/local/bin/parallel [04:43:43] Found freebayes - /usr/local/bin/freebayes [04:43:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:43:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:43:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:43:43] Found vcfuniq - /usr/local/bin/vcfuniq [04:43:43] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:43:43] Found gzip - /bin/gzip [04:43:43] Found vt - /usr/local/bin/vt [04:43:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:43:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:43:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:43:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:43:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:43:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:43:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:43:44] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:43:57] This is snippy 4.6.0
Show full stderr[04:43:57] This is snippy 4.6.0 [04:43:57] Written by Torsten Seemann [04:43:57] Obtained from https://github.com/tseemann/snippy [04:43:57] Detected operating system: linux [04:43:57] Enabling bundled linux tools. [04:43:57] Found bwa - /usr/local/bin/bwa [04:43:57] Found bcftools - /usr/local/bin/bcftools [04:43:57] Found samtools - /usr/local/bin/samtools [04:43:57] Found java - /usr/local/bin/java [04:43:57] Found snpEff - /usr/local/bin/snpEff [04:43:57] Found samclip - /usr/local/bin/samclip [04:43:57] Found seqtk - /usr/local/bin/seqtk [04:43:57] Found parallel - /usr/local/bin/parallel [04:43:57] Found freebayes - /usr/local/bin/freebayes [04:43:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:43:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:43:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:43:57] Found vcfuniq - /usr/local/bin/vcfuniq [04:43:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:43:57] Found gzip - /bin/gzip [04:43:57] Found vt - /usr/local/bin/vt [04:43:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:43:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:43:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:43:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:43:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:43:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:43:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:43:58] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:44:02] This is snippy 4.6.0
Show full stderr[04:44:02] This is snippy 4.6.0 [04:44:02] Written by Torsten Seemann [04:44:02] Obtained from https://github.com/tseemann/snippy [04:44:02] Detected operating system: linux [04:44:02] Enabling bundled linux tools. [04:44:02] Found bwa - /usr/local/bin/bwa [04:44:02] Found bcftools - /usr/local/bin/bcftools [04:44:02] Found samtools - /usr/local/bin/samtools [04:44:02] Found java - /usr/local/bin/java [04:44:02] Found snpEff - /usr/local/bin/snpEff [04:44:02] Found samclip - /usr/local/bin/samclip [04:44:02] Found seqtk - /usr/local/bin/seqtk [04:44:02] Found parallel - /usr/local/bin/parallel [04:44:02] Found freebayes - /usr/local/bin/freebayes [04:44:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:44:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:44:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:44:02] Found vcfuniq - /usr/local/bin/vcfuniq [04:44:02] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:44:02] Found gzip - /bin/gzip [04:44:02] Found vt - /usr/local/bin/vt [04:44:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:44:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:44:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:44:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:44:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:44:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:44:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:44:03] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:49:36] This is snippy 4.6.0
Show full stderr[04:49:36] This is snippy 4.6.0 [04:49:36] Written by Torsten Seemann [04:49:36] Obtained from https://github.com/tseemann/snippy [04:49:36] Detected operating system: linux [04:49:36] Enabling bundled linux tools. [04:49:36] Found bwa - /usr/local/bin/bwa [04:49:36] Found bcftools - /usr/local/bin/bcftools [04:49:36] Found samtools - /usr/local/bin/samtools [04:49:36] Found java - /usr/local/bin/java [04:49:36] Found snpEff - /usr/local/bin/snpEff [04:49:36] Found samclip - /usr/local/bin/samclip [04:49:36] Found seqtk - /usr/local/bin/seqtk [04:49:36] Found parallel - /usr/local/bin/parallel [04:49:36] Found freebayes - /usr/local/bin/freebayes [04:49:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:49:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:49:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:49:36] Found vcfuniq - /usr/local/bin/vcfuniq [04:49:36] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:49:36] Found gzip - /bin/gzip [04:49:36] Found vt - /usr/local/bin/vt [04:49:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:49:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:49:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:49:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:49:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:49:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:49:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:49:37] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:49:51] This is snippy 4.6.0
Show full stderr[04:49:51] This is snippy 4.6.0 [04:49:51] Written by Torsten Seemann [04:49:51] Obtained from https://github.com/tseemann/snippy [04:49:51] Detected operating system: linux [04:49:51] Enabling bundled linux tools. [04:49:51] Found bwa - /usr/local/bin/bwa [04:49:51] Found bcftools - /usr/local/bin/bcftools [04:49:51] Found samtools - /usr/local/bin/samtools [04:49:51] Found java - /usr/local/bin/java [04:49:51] Found snpEff - /usr/local/bin/snpEff [04:49:51] Found samclip - /usr/local/bin/samclip [04:49:51] Found seqtk - /usr/local/bin/seqtk [04:49:51] Found parallel - /usr/local/bin/parallel [04:49:51] Found freebayes - /usr/local/bin/freebayes [04:49:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:49:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:49:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:49:51] Found vcfuniq - /usr/local/bin/vcfuniq [04:49:51] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:49:51] Found gzip - /bin/gzip [04:49:51] Found vt - /usr/local/bin/vt [04:49:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:49:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:49:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:49:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:49:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:49:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:49:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:49:52] Please supply a reference FASTA/GBK/EMBL file with --reference
1[04:43:32] This is snippy 4.6.0
Show full stderr[04:43:32] This is snippy 4.6.0 [04:43:32] Written by Torsten Seemann [04:43:32] Obtained from https://github.com/tseemann/snippy [04:43:32] Detected operating system: linux [04:43:32] Enabling bundled linux tools. [04:43:32] Found bwa - /usr/local/bin/bwa [04:43:32] Found bcftools - /usr/local/bin/bcftools [04:43:32] Found samtools - /usr/local/bin/samtools [04:43:32] Found java - /usr/local/bin/java [04:43:32] Found snpEff - /usr/local/bin/snpEff [04:43:32] Found samclip - /usr/local/bin/samclip [04:43:32] Found seqtk - /usr/local/bin/seqtk [04:43:32] Found parallel - /usr/local/bin/parallel [04:43:32] Found freebayes - /usr/local/bin/freebayes [04:43:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [04:43:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [04:43:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [04:43:32] Found vcfuniq - /usr/local/bin/vcfuniq [04:43:32] Found vcffirstheader - /usr/local/bin/vcffirstheader [04:43:32] Found gzip - /bin/gzip [04:43:32] Found vt - /usr/local/bin/vt [04:43:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [04:43:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [04:43:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [04:43:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [04:43:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [04:43:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [04:43:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [04:43:39] Please supply a reference FASTA/GBK/EMBL file with --reference
1[10:24:53] This is snippy 4.6.0
Show full stderr[10:24:53] This is snippy 4.6.0 [10:24:53] Written by Torsten Seemann [10:24:53] Obtained from https://github.com/tseemann/snippy [10:24:53] Detected operating system: linux [10:24:53] Enabling bundled linux tools. [10:24:53] Found bwa - /usr/local/bin/bwa [10:24:53] Found bcftools - /usr/local/bin/bcftools [10:24:53] Found samtools - /usr/local/bin/samtools [10:24:53] Found java - /usr/local/bin/java [10:24:53] Found snpEff - /usr/local/bin/snpEff [10:24:53] Found samclip - /usr/local/bin/samclip [10:24:53] Found seqtk - /usr/local/bin/seqtk [10:24:53] Found parallel - /usr/local/bin/parallel [10:24:53] Found freebayes - /usr/local/bin/freebayes [10:24:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [10:24:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [10:24:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [10:24:53] Found vcfuniq - /usr/local/bin/vcfuniq [10:24:53] Found vcffirstheader - /usr/local/bin/vcffirstheader [10:24:53] Found gzip - /bin/gzip [10:24:53] Found vt - /usr/local/bin/vt [10:24:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [10:24:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [10:24:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [10:24:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [10:24:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [10:24:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [10:24:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [10:24:54] Using reference: /corral4/main/objects/2/6/3/dataset_2633c7de-ac59-4614-a6e1-1b68720a214a.dat [10:24:54] Treating reference as 'genbank' format. [10:24:54] Will use 1 CPU cores. [10:24:54] Using read file: /corral4/main/objects/7/c/7/dataset_7c76c421-2e73-43c8-a760-8db79445644b.dat [10:24:54] Creating folder: GCA_009734005_2_ASM973400v2_genomic_fna [10:24:54] Changing working directory: GCA_009734005_2_ASM973400v2_genomic_fna [10:24:54] Creating reference folder: reference [10:24:54] Extracting FASTA and GFF from reference. [10:24:55] Wrote 1 sequences to ref.fa [10:24:55] Wrote 1 features to ref.gff [10:24:55] Shredding /corral4/main/objects/7/c/7/dataset_7c76c421-2e73-43c8-a760-8db79445644b.dat into pseudo-reads [10:24:57] Wrote 233618 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [10:24:57] Creating reference/snpeff.config [10:24:57] Freebayes will process 1 chunks of 2951188 bp, 1 chunks at a time. [10:24:57] Using BAM RG (Read Group) ID: GCA_009734005_2_ASM973400v2_genomic_fna [10:24:57] Running: samtools faidx reference/ref.fa 2>> snps.log [10:24:57] Running: bwa index reference/ref.fa 2>> snps.log [10:24:58] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [10:24:58] Running: ln -sf reference/ref.fa . 2>> snps.log [10:24:58] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [10:24:58] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [10:24:58] Running: snpEff build -c reference/snpeff.config -dataDir . -gff3 ref 2>> snps.log [10:25:01] Error running command, check GCA_009734005_2_ASM973400v2_genomic_fna/snps.log
1[13:49:16] This is snippy 4.6.0
Show full stderr[13:49:16] This is snippy 4.6.0 [13:49:16] Written by Torsten Seemann [13:49:16] Obtained from https://github.com/tseemann/snippy [13:49:16] Detected operating system: linux [13:49:16] Enabling bundled linux tools. [13:49:16] Found bwa - /usr/local/bin/bwa [13:49:16] Found bcftools - /usr/local/bin/bcftools [13:49:16] Found samtools - /usr/local/bin/samtools [13:49:16] Found java - /usr/local/bin/java [13:49:16] Found snpEff - /usr/local/bin/snpEff [13:49:16] Found samclip - /usr/local/bin/samclip [13:49:16] Found seqtk - /usr/local/bin/seqtk [13:49:16] Found parallel - /usr/local/bin/parallel [13:49:16] Found freebayes - /usr/local/bin/freebayes [13:49:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [13:49:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [13:49:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [13:49:16] Found vcfuniq - /usr/local/bin/vcfuniq [13:49:16] Found vcffirstheader - /usr/local/bin/vcffirstheader [13:49:16] Found gzip - /bin/gzip [13:49:16] Found vt - /usr/local/bin/vt [13:49:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [13:49:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [13:49:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [13:49:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [13:49:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [13:49:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [13:49:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [13:49:17] Using reference: /jetstream2/scratch/main/jobs/72310760/inputs/dataset_c3278295-0534-4341-a983-519e27d93d98.dat [13:49:17] Treating reference as 'fasta' format. [13:49:17] Will use 1 CPU cores. [13:49:17] Using read file: /jetstream2/scratch/main/jobs/72310760/inputs/dataset_eaf88053-c6c7-4573-935e-0a20a2a2f029.dat [13:49:17] Creating folder: Select_on_dataset_11 [13:49:17] Changing working directory: Select_on_dataset_11 [13:49:17] Creating reference folder: reference [13:49:17] Extracting FASTA and GFF from reference. [13:49:17] Wrote 1 sequences to ref.fa [13:49:17] Wrote 0 features to ref.gff [13:49:17] Freebayes will process 1 chunks of 12416664 bp, 1 chunks at a time. [13:49:17] Using BAM RG (Read Group) ID: Select_on_dataset_11 [13:49:17] Running: samtools faidx reference/ref.fa 2>> snps.log [13:49:18] Running: bwa index reference/ref.fa 2>> snps.log [13:49:23] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [13:49:23] Running: ln -sf reference/ref.fa . 2>> snps.log [13:49:23] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [13:49:23] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [13:49:23] Running: bwa mem -Y -M -R '@RG\tID:Select_on_dataset_11\tSM:Select_on_dataset_11' -t 1 reference/ref.fa /jetstream2/scratch/main/jobs/72310760/inputs/dataset_eaf88053-c6c7-4573-935e-0a20a2a2f029.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/72310760/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/72310760/tmp --threads 0 -m 12000M | samtools markdup -T /jetstream2/scratch/main/jobs/72310760/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 1 sequences in reference/ref.fa.fai [M::process] read 1 sequences (11639536 bp)... [samclip] Total SAM records 0
1[09:46:52] This is snippy 4.6.0
Show full stderr[09:46:52] This is snippy 4.6.0 [09:46:52] Written by Torsten Seemann [09:46:52] Obtained from https://github.com/tseemann/snippy [09:46:52] Detected operating system: linux [09:46:52] Enabling bundled linux tools. [09:46:52] Found bwa - /usr/local/bin/bwa [09:46:52] Found bcftools - /usr/local/bin/bcftools [09:46:52] Found samtools - /usr/local/bin/samtools [09:46:52] Found java - /usr/local/bin/java [09:46:52] Found snpEff - /usr/local/bin/snpEff [09:46:52] Found samclip - /usr/local/bin/samclip [09:46:52] Found seqtk - /usr/local/bin/seqtk [09:46:52] Found parallel - /usr/local/bin/parallel [09:46:52] Found freebayes - /usr/local/bin/freebayes [09:46:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [09:46:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [09:46:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [09:46:52] Found vcfuniq - /usr/local/bin/vcfuniq [09:46:52] Found vcffirstheader - /usr/local/bin/vcffirstheader [09:46:52] Found gzip - /bin/gzip [09:46:52] Found vt - /usr/local/bin/vt [09:46:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [09:46:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [09:46:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [09:46:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [09:46:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [09:46:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [09:46:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [09:46:53] Please supply a reference FASTA/GBK/EMBL file with --reference
1[09:46:39] This is snippy 4.6.0
Show full stderr[09:46:39] This is snippy 4.6.0 [09:46:39] Written by Torsten Seemann [09:46:39] Obtained from https://github.com/tseemann/snippy [09:46:39] Detected operating system: linux [09:46:39] Enabling bundled linux tools. [09:46:39] Found bwa - /usr/local/bin/bwa [09:46:39] Found bcftools - /usr/local/bin/bcftools [09:46:39] Found samtools - /usr/local/bin/samtools [09:46:39] Found java - /usr/local/bin/java [09:46:39] Found snpEff - /usr/local/bin/snpEff [09:46:39] Found samclip - /usr/local/bin/samclip [09:46:39] Found seqtk - /usr/local/bin/seqtk [09:46:39] Found parallel - /usr/local/bin/parallel [09:46:39] Found freebayes - /usr/local/bin/freebayes [09:46:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [09:46:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [09:46:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [09:46:39] Found vcfuniq - /usr/local/bin/vcfuniq [09:46:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [09:46:39] Found gzip - /bin/gzip [09:46:39] Found vt - /usr/local/bin/vt [09:46:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [09:46:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [09:46:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [09:46:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [09:46:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [09:46:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [09:46:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [09:46:40] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:48:30] This is snippy 4.6.0
Show full stderr[12:48:30] This is snippy 4.6.0 [12:48:30] Written by Torsten Seemann [12:48:30] Obtained from https://github.com/tseemann/snippy [12:48:30] Detected operating system: linux [12:48:30] Enabling bundled linux tools. [12:48:30] Found bwa - /usr/local/bin/bwa [12:48:30] Found bcftools - /usr/local/bin/bcftools [12:48:30] Found samtools - /usr/local/bin/samtools [12:48:30] Found java - /usr/local/bin/java [12:48:30] Found snpEff - /usr/local/bin/snpEff [12:48:30] Found samclip - /usr/local/bin/samclip [12:48:30] Found seqtk - /usr/local/bin/seqtk [12:48:30] Found parallel - /usr/local/bin/parallel [12:48:30] Found freebayes - /usr/local/bin/freebayes [12:48:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:48:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:48:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:48:30] Found vcfuniq - /usr/local/bin/vcfuniq [12:48:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:48:30] Found gzip - /bin/gzip [12:48:30] Found vt - /usr/local/bin/vt [12:48:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:48:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:48:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:48:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:48:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:48:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:48:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:48:31] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:49:18] This is snippy 4.6.0
Show full stderr[12:49:18] This is snippy 4.6.0 [12:49:18] Written by Torsten Seemann [12:49:18] Obtained from https://github.com/tseemann/snippy [12:49:18] Detected operating system: linux [12:49:18] Enabling bundled linux tools. [12:49:18] Found bwa - /usr/local/bin/bwa [12:49:18] Found bcftools - /usr/local/bin/bcftools [12:49:18] Found samtools - /usr/local/bin/samtools [12:49:18] Found java - /usr/local/bin/java [12:49:18] Found snpEff - /usr/local/bin/snpEff [12:49:18] Found samclip - /usr/local/bin/samclip [12:49:18] Found seqtk - /usr/local/bin/seqtk [12:49:18] Found parallel - /usr/local/bin/parallel [12:49:18] Found freebayes - /usr/local/bin/freebayes [12:49:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:49:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:49:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:49:18] Found vcfuniq - /usr/local/bin/vcfuniq [12:49:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:49:18] Found gzip - /bin/gzip [12:49:18] Found vt - /usr/local/bin/vt [12:49:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:49:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:49:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:49:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:49:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:49:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:49:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:49:19] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:49:21] This is snippy 4.6.0
Show full stderr[12:49:21] This is snippy 4.6.0 [12:49:21] Written by Torsten Seemann [12:49:21] Obtained from https://github.com/tseemann/snippy [12:49:21] Detected operating system: linux [12:49:21] Enabling bundled linux tools. [12:49:21] Found bwa - /usr/local/bin/bwa [12:49:21] Found bcftools - /usr/local/bin/bcftools [12:49:21] Found samtools - /usr/local/bin/samtools [12:49:21] Found java - /usr/local/bin/java [12:49:21] Found snpEff - /usr/local/bin/snpEff [12:49:21] Found samclip - /usr/local/bin/samclip [12:49:21] Found seqtk - /usr/local/bin/seqtk [12:49:21] Found parallel - /usr/local/bin/parallel [12:49:21] Found freebayes - /usr/local/bin/freebayes [12:49:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:49:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:49:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:49:21] Found vcfuniq - /usr/local/bin/vcfuniq [12:49:21] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:49:21] Found gzip - /bin/gzip [12:49:21] Found vt - /usr/local/bin/vt [12:49:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:49:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:49:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:49:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:49:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:49:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:49:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:49:22] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:49:33] This is snippy 4.6.0
Show full stderr[12:49:33] This is snippy 4.6.0 [12:49:33] Written by Torsten Seemann [12:49:33] Obtained from https://github.com/tseemann/snippy [12:49:33] Detected operating system: linux [12:49:33] Enabling bundled linux tools. [12:49:33] Found bwa - /usr/local/bin/bwa [12:49:33] Found bcftools - /usr/local/bin/bcftools [12:49:33] Found samtools - /usr/local/bin/samtools [12:49:33] Found java - /usr/local/bin/java [12:49:33] Found snpEff - /usr/local/bin/snpEff [12:49:33] Found samclip - /usr/local/bin/samclip [12:49:33] Found seqtk - /usr/local/bin/seqtk [12:49:33] Found parallel - /usr/local/bin/parallel [12:49:33] Found freebayes - /usr/local/bin/freebayes [12:49:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:49:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:49:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:49:33] Found vcfuniq - /usr/local/bin/vcfuniq [12:49:33] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:49:33] Found gzip - /bin/gzip [12:49:33] Found vt - /usr/local/bin/vt [12:49:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:49:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:49:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:49:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:49:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:49:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:49:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:49:34] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:49:45] This is snippy 4.6.0
Show full stderr[12:49:45] This is snippy 4.6.0 [12:49:45] Written by Torsten Seemann [12:49:45] Obtained from https://github.com/tseemann/snippy [12:49:45] Detected operating system: linux [12:49:45] Enabling bundled linux tools. [12:49:45] Found bwa - /usr/local/bin/bwa [12:49:45] Found bcftools - /usr/local/bin/bcftools [12:49:45] Found samtools - /usr/local/bin/samtools [12:49:45] Found java - /usr/local/bin/java [12:49:45] Found snpEff - /usr/local/bin/snpEff [12:49:45] Found samclip - /usr/local/bin/samclip [12:49:45] Found seqtk - /usr/local/bin/seqtk [12:49:45] Found parallel - /usr/local/bin/parallel [12:49:45] Found freebayes - /usr/local/bin/freebayes [12:49:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:49:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:49:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:49:45] Found vcfuniq - /usr/local/bin/vcfuniq [12:49:45] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:49:45] Found gzip - /bin/gzip [12:49:45] Found vt - /usr/local/bin/vt [12:49:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:49:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:49:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:49:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:49:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:49:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:49:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:49:46] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:49:48] This is snippy 4.6.0
Show full stderr[12:49:48] This is snippy 4.6.0 [12:49:48] Written by Torsten Seemann [12:49:48] Obtained from https://github.com/tseemann/snippy [12:49:48] Detected operating system: linux [12:49:48] Enabling bundled linux tools. [12:49:48] Found bwa - /usr/local/bin/bwa [12:49:48] Found bcftools - /usr/local/bin/bcftools [12:49:48] Found samtools - /usr/local/bin/samtools [12:49:48] Found java - /usr/local/bin/java [12:49:48] Found snpEff - /usr/local/bin/snpEff [12:49:48] Found samclip - /usr/local/bin/samclip [12:49:48] Found seqtk - /usr/local/bin/seqtk [12:49:48] Found parallel - /usr/local/bin/parallel [12:49:48] Found freebayes - /usr/local/bin/freebayes [12:49:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:49:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:49:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:49:48] Found vcfuniq - /usr/local/bin/vcfuniq [12:49:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:49:48] Found gzip - /bin/gzip [12:49:48] Found vt - /usr/local/bin/vt [12:49:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:49:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:49:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:49:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:49:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:49:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:49:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:49:49] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:49:58] This is snippy 4.6.0
Show full stderr[12:49:58] This is snippy 4.6.0 [12:49:58] Written by Torsten Seemann [12:49:58] Obtained from https://github.com/tseemann/snippy [12:49:58] Detected operating system: linux [12:49:58] Enabling bundled linux tools. [12:49:58] Found bwa - /usr/local/bin/bwa [12:49:58] Found bcftools - /usr/local/bin/bcftools [12:49:58] Found samtools - /usr/local/bin/samtools [12:49:58] Found java - /usr/local/bin/java [12:49:58] Found snpEff - /usr/local/bin/snpEff [12:49:58] Found samclip - /usr/local/bin/samclip [12:49:58] Found seqtk - /usr/local/bin/seqtk [12:49:58] Found parallel - /usr/local/bin/parallel [12:49:58] Found freebayes - /usr/local/bin/freebayes [12:49:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:49:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:49:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:49:58] Found vcfuniq - /usr/local/bin/vcfuniq [12:49:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:49:58] Found gzip - /bin/gzip [12:49:58] Found vt - /usr/local/bin/vt [12:49:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:49:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:49:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:49:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:49:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:49:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:49:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:49:59] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:50:01] This is snippy 4.6.0
Show full stderr[12:50:01] This is snippy 4.6.0 [12:50:01] Written by Torsten Seemann [12:50:01] Obtained from https://github.com/tseemann/snippy [12:50:01] Detected operating system: linux [12:50:01] Enabling bundled linux tools. [12:50:01] Found bwa - /usr/local/bin/bwa [12:50:01] Found bcftools - /usr/local/bin/bcftools [12:50:01] Found samtools - /usr/local/bin/samtools [12:50:01] Found java - /usr/local/bin/java [12:50:01] Found snpEff - /usr/local/bin/snpEff [12:50:01] Found samclip - /usr/local/bin/samclip [12:50:01] Found seqtk - /usr/local/bin/seqtk [12:50:01] Found parallel - /usr/local/bin/parallel [12:50:01] Found freebayes - /usr/local/bin/freebayes [12:50:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:50:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:50:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:50:01] Found vcfuniq - /usr/local/bin/vcfuniq [12:50:01] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:50:01] Found gzip - /bin/gzip [12:50:01] Found vt - /usr/local/bin/vt [12:50:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:50:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:50:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:50:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:50:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:50:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:50:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:50:02] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:51:06] This is snippy 4.6.0
Show full stderr[12:51:06] This is snippy 4.6.0 [12:51:06] Written by Torsten Seemann [12:51:06] Obtained from https://github.com/tseemann/snippy [12:51:06] Detected operating system: linux [12:51:06] Enabling bundled linux tools. [12:51:06] Found bwa - /usr/local/bin/bwa [12:51:06] Found bcftools - /usr/local/bin/bcftools [12:51:06] Found samtools - /usr/local/bin/samtools [12:51:06] Found java - /usr/local/bin/java [12:51:06] Found snpEff - /usr/local/bin/snpEff [12:51:06] Found samclip - /usr/local/bin/samclip [12:51:06] Found seqtk - /usr/local/bin/seqtk [12:51:06] Found parallel - /usr/local/bin/parallel [12:51:06] Found freebayes - /usr/local/bin/freebayes [12:51:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:51:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:51:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:51:06] Found vcfuniq - /usr/local/bin/vcfuniq [12:51:06] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:51:06] Found gzip - /bin/gzip [12:51:06] Found vt - /usr/local/bin/vt [12:51:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:51:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:51:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:51:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:51:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:51:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:51:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:51:07] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:50:38] This is snippy 4.6.0
Show full stderr[12:50:38] This is snippy 4.6.0 [12:50:38] Written by Torsten Seemann [12:50:38] Obtained from https://github.com/tseemann/snippy [12:50:38] Detected operating system: linux [12:50:38] Enabling bundled linux tools. [12:50:38] Found bwa - /usr/local/bin/bwa [12:50:38] Found bcftools - /usr/local/bin/bcftools [12:50:38] Found samtools - /usr/local/bin/samtools [12:50:38] Found java - /usr/local/bin/java [12:50:38] Found snpEff - /usr/local/bin/snpEff [12:50:38] Found samclip - /usr/local/bin/samclip [12:50:38] Found seqtk - /usr/local/bin/seqtk [12:50:38] Found parallel - /usr/local/bin/parallel [12:50:38] Found freebayes - /usr/local/bin/freebayes [12:50:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:50:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:50:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:50:38] Found vcfuniq - /usr/local/bin/vcfuniq [12:50:38] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:50:38] Found gzip - /bin/gzip [12:50:38] Found vt - /usr/local/bin/vt [12:50:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:50:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:50:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:50:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:50:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:50:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:50:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:50:39] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:48:33] This is snippy 4.6.0
Show full stderr[12:48:33] This is snippy 4.6.0 [12:48:33] Written by Torsten Seemann [12:48:33] Obtained from https://github.com/tseemann/snippy [12:48:33] Detected operating system: linux [12:48:33] Enabling bundled linux tools. [12:48:33] Found bwa - /usr/local/bin/bwa [12:48:33] Found bcftools - /usr/local/bin/bcftools [12:48:33] Found samtools - /usr/local/bin/samtools [12:48:33] Found java - /usr/local/bin/java [12:48:33] Found snpEff - /usr/local/bin/snpEff [12:48:33] Found samclip - /usr/local/bin/samclip [12:48:33] Found seqtk - /usr/local/bin/seqtk [12:48:33] Found parallel - /usr/local/bin/parallel [12:48:33] Found freebayes - /usr/local/bin/freebayes [12:48:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:48:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:48:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:48:33] Found vcfuniq - /usr/local/bin/vcfuniq [12:48:33] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:48:33] Found gzip - /bin/gzip [12:48:33] Found vt - /usr/local/bin/vt [12:48:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:48:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:48:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:48:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:48:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:48:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:48:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:48:34] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:48:00] This is snippy 4.6.0
Show full stderr[12:48:00] This is snippy 4.6.0 [12:48:00] Written by Torsten Seemann [12:48:00] Obtained from https://github.com/tseemann/snippy [12:48:00] Detected operating system: linux [12:48:00] Enabling bundled linux tools. [12:48:00] Found bwa - /usr/local/bin/bwa [12:48:00] Found bcftools - /usr/local/bin/bcftools [12:48:00] Found samtools - /usr/local/bin/samtools [12:48:00] Found java - /usr/local/bin/java [12:48:00] Found snpEff - /usr/local/bin/snpEff [12:48:00] Found samclip - /usr/local/bin/samclip [12:48:00] Found seqtk - /usr/local/bin/seqtk [12:48:00] Found parallel - /usr/local/bin/parallel [12:48:00] Found freebayes - /usr/local/bin/freebayes [12:48:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:48:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:48:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:48:00] Found vcfuniq - /usr/local/bin/vcfuniq [12:48:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:48:00] Found gzip - /bin/gzip [12:48:00] Found vt - /usr/local/bin/vt [12:48:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:48:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:48:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:48:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:48:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:48:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:48:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:48:01] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:48:49] This is snippy 4.6.0
Show full stderr[12:48:49] This is snippy 4.6.0 [12:48:49] Written by Torsten Seemann [12:48:49] Obtained from https://github.com/tseemann/snippy [12:48:49] Detected operating system: linux [12:48:49] Enabling bundled linux tools. [12:48:49] Found bwa - /usr/local/bin/bwa [12:48:49] Found bcftools - /usr/local/bin/bcftools [12:48:49] Found samtools - /usr/local/bin/samtools [12:48:49] Found java - /usr/local/bin/java [12:48:49] Found snpEff - /usr/local/bin/snpEff [12:48:49] Found samclip - /usr/local/bin/samclip [12:48:49] Found seqtk - /usr/local/bin/seqtk [12:48:49] Found parallel - /usr/local/bin/parallel [12:48:49] Found freebayes - /usr/local/bin/freebayes [12:48:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:48:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:48:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:48:49] Found vcfuniq - /usr/local/bin/vcfuniq [12:48:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:48:49] Found gzip - /bin/gzip [12:48:49] Found vt - /usr/local/bin/vt [12:48:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:48:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:48:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:48:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:48:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:48:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:48:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:48:50] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:48:40] This is snippy 4.6.0
Show full stderr[12:48:40] This is snippy 4.6.0 [12:48:40] Written by Torsten Seemann [12:48:40] Obtained from https://github.com/tseemann/snippy [12:48:40] Detected operating system: linux [12:48:40] Enabling bundled linux tools. [12:48:40] Found bwa - /usr/local/bin/bwa [12:48:40] Found bcftools - /usr/local/bin/bcftools [12:48:40] Found samtools - /usr/local/bin/samtools [12:48:40] Found java - /usr/local/bin/java [12:48:40] Found snpEff - /usr/local/bin/snpEff [12:48:40] Found samclip - /usr/local/bin/samclip [12:48:40] Found seqtk - /usr/local/bin/seqtk [12:48:40] Found parallel - /usr/local/bin/parallel [12:48:40] Found freebayes - /usr/local/bin/freebayes [12:48:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:48:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:48:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:48:40] Found vcfuniq - /usr/local/bin/vcfuniq [12:48:40] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:48:40] Found gzip - /bin/gzip [12:48:40] Found vt - /usr/local/bin/vt [12:48:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:48:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:48:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:48:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:48:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:48:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:48:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:48:41] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:50:18] This is snippy 4.6.0
Show full stderr[12:50:18] This is snippy 4.6.0 [12:50:18] Written by Torsten Seemann [12:50:18] Obtained from https://github.com/tseemann/snippy [12:50:18] Detected operating system: linux [12:50:18] Enabling bundled linux tools. [12:50:18] Found bwa - /usr/local/bin/bwa [12:50:18] Found bcftools - /usr/local/bin/bcftools [12:50:18] Found samtools - /usr/local/bin/samtools [12:50:18] Found java - /usr/local/bin/java [12:50:18] Found snpEff - /usr/local/bin/snpEff [12:50:18] Found samclip - /usr/local/bin/samclip [12:50:18] Found seqtk - /usr/local/bin/seqtk [12:50:18] Found parallel - /usr/local/bin/parallel [12:50:18] Found freebayes - /usr/local/bin/freebayes [12:50:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:50:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:50:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:50:18] Found vcfuniq - /usr/local/bin/vcfuniq [12:50:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:50:18] Found gzip - /bin/gzip [12:50:18] Found vt - /usr/local/bin/vt [12:50:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:50:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:50:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:50:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:50:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:50:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:50:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:50:22] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:49:01] This is snippy 4.6.0
Show full stderr[12:49:01] This is snippy 4.6.0 [12:49:01] Written by Torsten Seemann [12:49:01] Obtained from https://github.com/tseemann/snippy [12:49:01] Detected operating system: linux [12:49:01] Enabling bundled linux tools. [12:49:01] Found bwa - /usr/local/bin/bwa [12:49:01] Found bcftools - /usr/local/bin/bcftools [12:49:01] Found samtools - /usr/local/bin/samtools [12:49:01] Found java - /usr/local/bin/java [12:49:01] Found snpEff - /usr/local/bin/snpEff [12:49:01] Found samclip - /usr/local/bin/samclip [12:49:01] Found seqtk - /usr/local/bin/seqtk [12:49:01] Found parallel - /usr/local/bin/parallel [12:49:01] Found freebayes - /usr/local/bin/freebayes [12:49:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:49:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:49:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:49:01] Found vcfuniq - /usr/local/bin/vcfuniq [12:49:01] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:49:01] Found gzip - /bin/gzip [12:49:01] Found vt - /usr/local/bin/vt [12:49:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:49:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:49:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:49:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:49:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:49:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:49:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:49:02] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:49:39] This is snippy 4.6.0
Show full stderr[12:49:39] This is snippy 4.6.0 [12:49:39] Written by Torsten Seemann [12:49:39] Obtained from https://github.com/tseemann/snippy [12:49:39] Detected operating system: linux [12:49:39] Enabling bundled linux tools. [12:49:39] Found bwa - /usr/local/bin/bwa [12:49:39] Found bcftools - /usr/local/bin/bcftools [12:49:39] Found samtools - /usr/local/bin/samtools [12:49:39] Found java - /usr/local/bin/java [12:49:39] Found snpEff - /usr/local/bin/snpEff [12:49:39] Found samclip - /usr/local/bin/samclip [12:49:39] Found seqtk - /usr/local/bin/seqtk [12:49:39] Found parallel - /usr/local/bin/parallel [12:49:39] Found freebayes - /usr/local/bin/freebayes [12:49:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:49:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:49:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:49:39] Found vcfuniq - /usr/local/bin/vcfuniq [12:49:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:49:39] Found gzip - /bin/gzip [12:49:39] Found vt - /usr/local/bin/vt [12:49:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:49:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:49:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:49:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:49:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:49:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:49:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:49:40] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:56:47] This is snippy 4.6.0
Show full stderr[12:56:47] This is snippy 4.6.0 [12:56:47] Written by Torsten Seemann [12:56:47] Obtained from https://github.com/tseemann/snippy [12:56:47] Detected operating system: linux [12:56:47] Enabling bundled linux tools. [12:56:47] Found bwa - /usr/local/bin/bwa [12:56:47] Found bcftools - /usr/local/bin/bcftools [12:56:47] Found samtools - /usr/local/bin/samtools [12:56:47] Found java - /usr/local/bin/java [12:56:47] Found snpEff - /usr/local/bin/snpEff [12:56:47] Found samclip - /usr/local/bin/samclip [12:56:47] Found seqtk - /usr/local/bin/seqtk [12:56:47] Found parallel - /usr/local/bin/parallel [12:56:47] Found freebayes - /usr/local/bin/freebayes [12:56:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:56:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:56:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:56:47] Found vcfuniq - /usr/local/bin/vcfuniq [12:56:47] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:56:47] Found gzip - /bin/gzip [12:56:47] Found vt - /usr/local/bin/vt [12:56:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:56:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:56:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:56:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:56:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:56:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:56:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:56:48] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:57:17] This is snippy 4.6.0
Show full stderr[12:57:17] This is snippy 4.6.0 [12:57:17] Written by Torsten Seemann [12:57:17] Obtained from https://github.com/tseemann/snippy [12:57:17] Detected operating system: linux [12:57:17] Enabling bundled linux tools. [12:57:17] Found bwa - /usr/local/bin/bwa [12:57:17] Found bcftools - /usr/local/bin/bcftools [12:57:17] Found samtools - /usr/local/bin/samtools [12:57:17] Found java - /usr/local/bin/java [12:57:17] Found snpEff - /usr/local/bin/snpEff [12:57:17] Found samclip - /usr/local/bin/samclip [12:57:17] Found seqtk - /usr/local/bin/seqtk [12:57:17] Found parallel - /usr/local/bin/parallel [12:57:17] Found freebayes - /usr/local/bin/freebayes [12:57:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:57:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:57:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:57:17] Found vcfuniq - /usr/local/bin/vcfuniq [12:57:17] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:57:17] Found gzip - /bin/gzip [12:57:17] Found vt - /usr/local/bin/vt [12:57:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:57:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:57:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:57:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:57:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:57:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:57:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:57:17] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:49:30] This is snippy 4.6.0
Show full stderr[12:49:30] This is snippy 4.6.0 [12:49:30] Written by Torsten Seemann [12:49:30] Obtained from https://github.com/tseemann/snippy [12:49:30] Detected operating system: linux [12:49:30] Enabling bundled linux tools. [12:49:30] Found bwa - /usr/local/bin/bwa [12:49:30] Found bcftools - /usr/local/bin/bcftools [12:49:30] Found samtools - /usr/local/bin/samtools [12:49:30] Found java - /usr/local/bin/java [12:49:30] Found snpEff - /usr/local/bin/snpEff [12:49:30] Found samclip - /usr/local/bin/samclip [12:49:30] Found seqtk - /usr/local/bin/seqtk [12:49:30] Found parallel - /usr/local/bin/parallel [12:49:30] Found freebayes - /usr/local/bin/freebayes [12:49:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:49:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:49:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:49:30] Found vcfuniq - /usr/local/bin/vcfuniq [12:49:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:49:30] Found gzip - /bin/gzip [12:49:30] Found vt - /usr/local/bin/vt [12:49:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:49:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:49:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:49:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:49:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:49:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:49:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:49:31] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:58:07] This is snippy 4.6.0
Show full stderr[12:58:07] This is snippy 4.6.0 [12:58:07] Written by Torsten Seemann [12:58:07] Obtained from https://github.com/tseemann/snippy [12:58:07] Detected operating system: linux [12:58:07] Enabling bundled linux tools. [12:58:07] Found bwa - /usr/local/bin/bwa [12:58:07] Found bcftools - /usr/local/bin/bcftools [12:58:07] Found samtools - /usr/local/bin/samtools [12:58:07] Found java - /usr/local/bin/java [12:58:07] Found snpEff - /usr/local/bin/snpEff [12:58:07] Found samclip - /usr/local/bin/samclip [12:58:07] Found seqtk - /usr/local/bin/seqtk [12:58:07] Found parallel - /usr/local/bin/parallel [12:58:07] Found freebayes - /usr/local/bin/freebayes [12:58:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:58:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:58:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:58:07] Found vcfuniq - /usr/local/bin/vcfuniq [12:58:07] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:58:07] Found gzip - /bin/gzip [12:58:07] Found vt - /usr/local/bin/vt [12:58:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:58:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:58:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:58:08] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:58:08] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:58:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:58:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:58:08] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:54:25] This is snippy 4.6.0
Show full stderr[12:54:25] This is snippy 4.6.0 [12:54:25] Written by Torsten Seemann [12:54:25] Obtained from https://github.com/tseemann/snippy [12:54:25] Detected operating system: linux [12:54:25] Enabling bundled linux tools. [12:54:25] Found bwa - /usr/local/bin/bwa [12:54:25] Found bcftools - /usr/local/bin/bcftools [12:54:25] Found samtools - /usr/local/bin/samtools [12:54:25] Found java - /usr/local/bin/java [12:54:25] Found snpEff - /usr/local/bin/snpEff [12:54:25] Found samclip - /usr/local/bin/samclip [12:54:26] Found seqtk - /usr/local/bin/seqtk [12:54:26] Found parallel - /usr/local/bin/parallel [12:54:26] Found freebayes - /usr/local/bin/freebayes [12:54:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:54:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:54:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:54:26] Found vcfuniq - /usr/local/bin/vcfuniq [12:54:26] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:54:26] Found gzip - /bin/gzip [12:54:26] Found vt - /usr/local/bin/vt [12:54:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:54:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:54:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:54:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:54:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:54:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:54:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:54:27] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:57:46] This is snippy 4.6.0
Show full stderr[12:57:46] This is snippy 4.6.0 [12:57:46] Written by Torsten Seemann [12:57:46] Obtained from https://github.com/tseemann/snippy [12:57:46] Detected operating system: linux [12:57:46] Enabling bundled linux tools. [12:57:46] Found bwa - /usr/local/bin/bwa [12:57:46] Found bcftools - /usr/local/bin/bcftools [12:57:46] Found samtools - /usr/local/bin/samtools [12:57:46] Found java - /usr/local/bin/java [12:57:46] Found snpEff - /usr/local/bin/snpEff [12:57:46] Found samclip - /usr/local/bin/samclip [12:57:46] Found seqtk - /usr/local/bin/seqtk [12:57:46] Found parallel - /usr/local/bin/parallel [12:57:46] Found freebayes - /usr/local/bin/freebayes [12:57:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:57:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:57:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:57:46] Found vcfuniq - /usr/local/bin/vcfuniq [12:57:46] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:57:46] Found gzip - /bin/gzip [12:57:46] Found vt - /usr/local/bin/vt [12:57:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:57:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:57:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:57:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:57:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:57:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:57:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:57:47] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:58:17] This is snippy 4.6.0
Show full stderr[12:58:17] This is snippy 4.6.0 [12:58:17] Written by Torsten Seemann [12:58:17] Obtained from https://github.com/tseemann/snippy [12:58:17] Detected operating system: linux [12:58:17] Enabling bundled linux tools. [12:58:17] Found bwa - /usr/local/bin/bwa [12:58:17] Found bcftools - /usr/local/bin/bcftools [12:58:17] Found samtools - /usr/local/bin/samtools [12:58:17] Found java - /usr/local/bin/java [12:58:17] Found snpEff - /usr/local/bin/snpEff [12:58:17] Found samclip - /usr/local/bin/samclip [12:58:17] Found seqtk - /usr/local/bin/seqtk [12:58:17] Found parallel - /usr/local/bin/parallel [12:58:17] Found freebayes - /usr/local/bin/freebayes [12:58:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:58:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:58:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:58:17] Found vcfuniq - /usr/local/bin/vcfuniq [12:58:17] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:58:17] Found gzip - /bin/gzip [12:58:17] Found vt - /usr/local/bin/vt [12:58:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:58:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:58:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:58:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:58:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:58:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:58:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:58:18] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:54:35] This is snippy 4.6.0
Show full stderr[12:54:35] This is snippy 4.6.0 [12:54:35] Written by Torsten Seemann [12:54:35] Obtained from https://github.com/tseemann/snippy [12:54:35] Detected operating system: linux [12:54:35] Enabling bundled linux tools. [12:54:35] Found bwa - /usr/local/bin/bwa [12:54:35] Found bcftools - /usr/local/bin/bcftools [12:54:35] Found samtools - /usr/local/bin/samtools [12:54:35] Found java - /usr/local/bin/java [12:54:35] Found snpEff - /usr/local/bin/snpEff [12:54:35] Found samclip - /usr/local/bin/samclip [12:54:35] Found seqtk - /usr/local/bin/seqtk [12:54:35] Found parallel - /usr/local/bin/parallel [12:54:35] Found freebayes - /usr/local/bin/freebayes [12:54:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:54:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:54:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:54:35] Found vcfuniq - /usr/local/bin/vcfuniq [12:54:35] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:54:35] Found gzip - /bin/gzip [12:54:35] Found vt - /usr/local/bin/vt [12:54:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:54:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:54:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:54:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:54:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:54:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:54:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:54:36] Please supply a reference FASTA/GBK/EMBL file with --reference
1[13:04:03] This is snippy 4.6.0
Show full stderr[13:04:03] This is snippy 4.6.0 [13:04:03] Written by Torsten Seemann [13:04:03] Obtained from https://github.com/tseemann/snippy [13:04:03] Detected operating system: linux [13:04:03] Enabling bundled linux tools. [13:04:03] Found bwa - /usr/local/bin/bwa [13:04:03] Found bcftools - /usr/local/bin/bcftools [13:04:03] Found samtools - /usr/local/bin/samtools [13:04:03] Found java - /usr/local/bin/java [13:04:03] Found snpEff - /usr/local/bin/snpEff [13:04:03] Found samclip - /usr/local/bin/samclip [13:04:03] Found seqtk - /usr/local/bin/seqtk [13:04:03] Found parallel - /usr/local/bin/parallel [13:04:03] Found freebayes - /usr/local/bin/freebayes [13:04:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [13:04:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [13:04:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [13:04:03] Found vcfuniq - /usr/local/bin/vcfuniq [13:04:03] Found vcffirstheader - /usr/local/bin/vcffirstheader [13:04:03] Found gzip - /bin/gzip [13:04:03] Found vt - /usr/local/bin/vt [13:04:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [13:04:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [13:04:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [13:04:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [13:04:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [13:04:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [13:04:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [13:04:04] Please supply a reference FASTA/GBK/EMBL file with --reference
1[13:09:47] This is snippy 4.6.0
Show full stderr[13:09:47] This is snippy 4.6.0 [13:09:47] Written by Torsten Seemann [13:09:47] Obtained from https://github.com/tseemann/snippy [13:09:47] Detected operating system: linux [13:09:47] Enabling bundled linux tools. [13:09:47] Found bwa - /usr/local/bin/bwa [13:09:47] Found bcftools - /usr/local/bin/bcftools [13:09:47] Found samtools - /usr/local/bin/samtools [13:09:47] Found java - /usr/local/bin/java [13:09:47] Found snpEff - /usr/local/bin/snpEff [13:09:47] Found samclip - /usr/local/bin/samclip [13:09:47] Found seqtk - /usr/local/bin/seqtk [13:09:47] Found parallel - /usr/local/bin/parallel [13:09:47] Found freebayes - /usr/local/bin/freebayes [13:09:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [13:09:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [13:09:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [13:09:47] Found vcfuniq - /usr/local/bin/vcfuniq [13:09:47] Found vcffirstheader - /usr/local/bin/vcffirstheader [13:09:47] Found gzip - /bin/gzip [13:09:47] Found vt - /usr/local/bin/vt [13:09:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [13:09:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [13:09:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [13:09:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [13:09:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [13:09:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [13:09:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [13:09:48] Please supply a reference FASTA/GBK/EMBL file with --reference
1[13:10:49] This is snippy 4.6.0
Show full stderr[13:10:49] This is snippy 4.6.0 [13:10:49] Written by Torsten Seemann [13:10:49] Obtained from https://github.com/tseemann/snippy [13:10:49] Detected operating system: linux [13:10:49] Enabling bundled linux tools. [13:10:49] Found bwa - /usr/local/bin/bwa [13:10:49] Found bcftools - /usr/local/bin/bcftools [13:10:49] Found samtools - /usr/local/bin/samtools [13:10:49] Found java - /usr/local/bin/java [13:10:49] Found snpEff - /usr/local/bin/snpEff [13:10:49] Found samclip - /usr/local/bin/samclip [13:10:49] Found seqtk - /usr/local/bin/seqtk [13:10:49] Found parallel - /usr/local/bin/parallel [13:10:49] Found freebayes - /usr/local/bin/freebayes [13:10:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [13:10:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [13:10:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [13:10:49] Found vcfuniq - /usr/local/bin/vcfuniq [13:10:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [13:10:49] Found gzip - /bin/gzip [13:10:49] Found vt - /usr/local/bin/vt [13:10:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [13:10:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [13:10:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [13:10:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [13:10:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [13:10:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [13:10:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [13:10:49] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:55:19] This is snippy 4.6.0
Show full stderr[12:55:19] This is snippy 4.6.0 [12:55:19] Written by Torsten Seemann [12:55:19] Obtained from https://github.com/tseemann/snippy [12:55:19] Detected operating system: linux [12:55:19] Enabling bundled linux tools. [12:55:19] Found bwa - /usr/local/bin/bwa [12:55:19] Found bcftools - /usr/local/bin/bcftools [12:55:19] Found samtools - /usr/local/bin/samtools [12:55:19] Found java - /usr/local/bin/java [12:55:20] Found snpEff - /usr/local/bin/snpEff [12:55:20] Found samclip - /usr/local/bin/samclip [12:55:20] Found seqtk - /usr/local/bin/seqtk [12:55:20] Found parallel - /usr/local/bin/parallel [12:55:20] Found freebayes - /usr/local/bin/freebayes [12:55:20] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:55:20] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:55:20] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:55:20] Found vcfuniq - /usr/local/bin/vcfuniq [12:55:20] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:55:20] Found gzip - /bin/gzip [12:55:20] Found vt - /usr/local/bin/vt [12:55:20] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:55:20] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:55:20] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:55:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:55:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:55:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:55:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:55:20] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:51:03] This is snippy 4.6.0
Show full stderr[12:51:03] This is snippy 4.6.0 [12:51:03] Written by Torsten Seemann [12:51:03] Obtained from https://github.com/tseemann/snippy [12:51:03] Detected operating system: linux [12:51:03] Enabling bundled linux tools. [12:51:03] Found bwa - /usr/local/bin/bwa [12:51:03] Found bcftools - /usr/local/bin/bcftools [12:51:03] Found samtools - /usr/local/bin/samtools [12:51:03] Found java - /usr/local/bin/java [12:51:03] Found snpEff - /usr/local/bin/snpEff [12:51:03] Found samclip - /usr/local/bin/samclip [12:51:03] Found seqtk - /usr/local/bin/seqtk [12:51:03] Found parallel - /usr/local/bin/parallel [12:51:03] Found freebayes - /usr/local/bin/freebayes [12:51:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:51:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:51:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:51:03] Found vcfuniq - /usr/local/bin/vcfuniq [12:51:03] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:51:03] Found gzip - /bin/gzip [12:51:03] Found vt - /usr/local/bin/vt [12:51:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:51:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:51:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:51:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:51:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:51:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:51:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:51:04] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:56:41] This is snippy 4.6.0
Show full stderr[12:56:41] This is snippy 4.6.0 [12:56:41] Written by Torsten Seemann [12:56:41] Obtained from https://github.com/tseemann/snippy [12:56:41] Detected operating system: linux [12:56:41] Enabling bundled linux tools. [12:56:41] Found bwa - /usr/local/bin/bwa [12:56:41] Found bcftools - /usr/local/bin/bcftools [12:56:41] Found samtools - /usr/local/bin/samtools [12:56:41] Found java - /usr/local/bin/java [12:56:41] Found snpEff - /usr/local/bin/snpEff [12:56:41] Found samclip - /usr/local/bin/samclip [12:56:41] Found seqtk - /usr/local/bin/seqtk [12:56:41] Found parallel - /usr/local/bin/parallel [12:56:41] Found freebayes - /usr/local/bin/freebayes [12:56:41] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:56:41] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:56:41] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:56:41] Found vcfuniq - /usr/local/bin/vcfuniq [12:56:41] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:56:41] Found gzip - /bin/gzip [12:56:41] Found vt - /usr/local/bin/vt [12:56:41] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:56:41] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:56:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:56:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:56:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:56:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:56:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:56:42] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:57:42] This is snippy 4.6.0
Show full stderr[12:57:42] This is snippy 4.6.0 [12:57:42] Written by Torsten Seemann [12:57:42] Obtained from https://github.com/tseemann/snippy [12:57:42] Detected operating system: linux [12:57:42] Enabling bundled linux tools. [12:57:42] Found bwa - /usr/local/bin/bwa [12:57:42] Found bcftools - /usr/local/bin/bcftools [12:57:42] Found samtools - /usr/local/bin/samtools [12:57:42] Found java - /usr/local/bin/java [12:57:42] Found snpEff - /usr/local/bin/snpEff [12:57:42] Found samclip - /usr/local/bin/samclip [12:57:42] Found seqtk - /usr/local/bin/seqtk [12:57:42] Found parallel - /usr/local/bin/parallel [12:57:42] Found freebayes - /usr/local/bin/freebayes [12:57:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:57:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:57:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:57:42] Found vcfuniq - /usr/local/bin/vcfuniq [12:57:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:57:42] Found gzip - /bin/gzip [12:57:42] Found vt - /usr/local/bin/vt [12:57:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:57:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:57:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:57:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:57:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:57:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:57:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:57:48] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:56:53] This is snippy 4.6.0
Show full stderr[12:56:53] This is snippy 4.6.0 [12:56:53] Written by Torsten Seemann [12:56:53] Obtained from https://github.com/tseemann/snippy [12:56:53] Detected operating system: linux [12:56:53] Enabling bundled linux tools. [12:56:53] Found bwa - /usr/local/bin/bwa [12:56:53] Found bcftools - /usr/local/bin/bcftools [12:56:53] Found samtools - /usr/local/bin/samtools [12:56:53] Found java - /usr/local/bin/java [12:56:53] Found snpEff - /usr/local/bin/snpEff [12:56:53] Found samclip - /usr/local/bin/samclip [12:56:53] Found seqtk - /usr/local/bin/seqtk [12:56:53] Found parallel - /usr/local/bin/parallel [12:56:53] Found freebayes - /usr/local/bin/freebayes [12:56:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:56:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:56:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:56:53] Found vcfuniq - /usr/local/bin/vcfuniq [12:56:53] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:56:53] Found gzip - /bin/gzip [12:56:53] Found vt - /usr/local/bin/vt [12:56:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:56:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:56:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:56:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:56:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:56:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:56:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:56:53] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:57:06] This is snippy 4.6.0
Show full stderr[12:57:06] This is snippy 4.6.0 [12:57:06] Written by Torsten Seemann [12:57:06] Obtained from https://github.com/tseemann/snippy [12:57:06] Detected operating system: linux [12:57:06] Enabling bundled linux tools. [12:57:06] Found bwa - /usr/local/bin/bwa [12:57:06] Found bcftools - /usr/local/bin/bcftools [12:57:06] Found samtools - /usr/local/bin/samtools [12:57:06] Found java - /usr/local/bin/java [12:57:06] Found snpEff - /usr/local/bin/snpEff [12:57:06] Found samclip - /usr/local/bin/samclip [12:57:06] Found seqtk - /usr/local/bin/seqtk [12:57:06] Found parallel - /usr/local/bin/parallel [12:57:06] Found freebayes - /usr/local/bin/freebayes [12:57:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:57:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:57:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:57:06] Found vcfuniq - /usr/local/bin/vcfuniq [12:57:06] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:57:06] Found gzip - /bin/gzip [12:57:06] Found vt - /usr/local/bin/vt [12:57:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:57:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:57:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:57:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:57:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:57:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:57:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:57:06] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:58:15] This is snippy 4.6.0
Show full stderr[12:58:15] This is snippy 4.6.0 [12:58:15] Written by Torsten Seemann [12:58:15] Obtained from https://github.com/tseemann/snippy [12:58:15] Detected operating system: linux [12:58:15] Enabling bundled linux tools. [12:58:15] Found bwa - /usr/local/bin/bwa [12:58:15] Found bcftools - /usr/local/bin/bcftools [12:58:15] Found samtools - /usr/local/bin/samtools [12:58:15] Found java - /usr/local/bin/java [12:58:15] Found snpEff - /usr/local/bin/snpEff [12:58:15] Found samclip - /usr/local/bin/samclip [12:58:15] Found seqtk - /usr/local/bin/seqtk [12:58:15] Found parallel - /usr/local/bin/parallel [12:58:15] Found freebayes - /usr/local/bin/freebayes [12:58:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:58:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:58:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:58:15] Found vcfuniq - /usr/local/bin/vcfuniq [12:58:15] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:58:15] Found gzip - /bin/gzip [12:58:15] Found vt - /usr/local/bin/vt [12:58:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:58:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:58:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:58:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:58:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:58:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:58:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:58:16] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:58:03] This is snippy 4.6.0
Show full stderr[12:58:03] This is snippy 4.6.0 [12:58:03] Written by Torsten Seemann [12:58:03] Obtained from https://github.com/tseemann/snippy [12:58:03] Detected operating system: linux [12:58:03] Enabling bundled linux tools. [12:58:03] Found bwa - /usr/local/bin/bwa [12:58:03] Found bcftools - /usr/local/bin/bcftools [12:58:03] Found samtools - /usr/local/bin/samtools [12:58:03] Found java - /usr/local/bin/java [12:58:03] Found snpEff - /usr/local/bin/snpEff [12:58:03] Found samclip - /usr/local/bin/samclip [12:58:03] Found seqtk - /usr/local/bin/seqtk [12:58:03] Found parallel - /usr/local/bin/parallel [12:58:03] Found freebayes - /usr/local/bin/freebayes [12:58:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:58:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:58:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:58:03] Found vcfuniq - /usr/local/bin/vcfuniq [12:58:03] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:58:03] Found gzip - /bin/gzip [12:58:03] Found vt - /usr/local/bin/vt [12:58:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:58:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:58:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:58:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:58:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:58:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:58:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:58:04] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:48:58] This is snippy 4.6.0
Show full stderr[12:48:58] This is snippy 4.6.0 [12:48:58] Written by Torsten Seemann [12:48:58] Obtained from https://github.com/tseemann/snippy [12:48:58] Detected operating system: linux [12:48:58] Enabling bundled linux tools. [12:48:58] Found bwa - /usr/local/bin/bwa [12:48:58] Found bcftools - /usr/local/bin/bcftools [12:48:58] Found samtools - /usr/local/bin/samtools [12:48:58] Found java - /usr/local/bin/java [12:48:58] Found snpEff - /usr/local/bin/snpEff [12:48:58] Found samclip - /usr/local/bin/samclip [12:48:58] Found seqtk - /usr/local/bin/seqtk [12:48:58] Found parallel - /usr/local/bin/parallel [12:48:58] Found freebayes - /usr/local/bin/freebayes [12:48:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:48:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:48:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:48:58] Found vcfuniq - /usr/local/bin/vcfuniq [12:48:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:48:58] Found gzip - /bin/gzip [12:48:58] Found vt - /usr/local/bin/vt [12:48:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:48:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:48:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:48:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:48:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:48:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:48:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:48:59] Please supply a reference FASTA/GBK/EMBL file with --reference
1[13:23:55] This is snippy 4.6.0
Show full stderr[13:23:55] This is snippy 4.6.0 [13:23:55] Written by Torsten Seemann [13:23:55] Obtained from https://github.com/tseemann/snippy [13:23:55] Detected operating system: linux [13:23:55] Enabling bundled linux tools. [13:23:55] Found bwa - /usr/local/bin/bwa [13:23:55] Found bcftools - /usr/local/bin/bcftools [13:23:55] Found samtools - /usr/local/bin/samtools [13:23:55] Found java - /usr/local/bin/java [13:23:55] Found snpEff - /usr/local/bin/snpEff [13:23:55] Found samclip - /usr/local/bin/samclip [13:23:55] Found seqtk - /usr/local/bin/seqtk [13:23:55] Found parallel - /usr/local/bin/parallel [13:23:55] Found freebayes - /usr/local/bin/freebayes [13:23:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [13:23:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [13:23:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [13:23:55] Found vcfuniq - /usr/local/bin/vcfuniq [13:23:55] Found vcffirstheader - /usr/local/bin/vcffirstheader [13:23:55] Found gzip - /bin/gzip [13:23:55] Found vt - /usr/local/bin/vt [13:23:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [13:23:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [13:23:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [13:23:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [13:23:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [13:24:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [13:24:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [13:24:01] Please supply a reference FASTA/GBK/EMBL file with --reference
1[13:17:51] This is snippy 4.6.0
Show full stderr[13:17:51] This is snippy 4.6.0 [13:17:51] Written by Torsten Seemann [13:17:51] Obtained from https://github.com/tseemann/snippy [13:17:51] Detected operating system: linux [13:17:51] Enabling bundled linux tools. [13:17:51] Found bwa - /usr/local/bin/bwa [13:17:51] Found bcftools - /usr/local/bin/bcftools [13:17:51] Found samtools - /usr/local/bin/samtools [13:17:51] Found java - /usr/local/bin/java [13:17:51] Found snpEff - /usr/local/bin/snpEff [13:17:51] Found samclip - /usr/local/bin/samclip [13:17:51] Found seqtk - /usr/local/bin/seqtk [13:17:51] Found parallel - /usr/local/bin/parallel [13:17:51] Found freebayes - /usr/local/bin/freebayes [13:17:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [13:17:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [13:17:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [13:17:51] Found vcfuniq - /usr/local/bin/vcfuniq [13:17:51] Found vcffirstheader - /usr/local/bin/vcffirstheader [13:17:51] Found gzip - /bin/gzip [13:17:51] Found vt - /usr/local/bin/vt [13:17:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [13:17:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [13:17:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [13:17:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [13:17:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [13:17:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [13:17:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [13:17:52] Please supply a reference FASTA/GBK/EMBL file with --reference
1[13:24:07] This is snippy 4.6.0
Show full stderr[13:24:07] This is snippy 4.6.0 [13:24:07] Written by Torsten Seemann [13:24:07] Obtained from https://github.com/tseemann/snippy [13:24:07] Detected operating system: linux [13:24:07] Enabling bundled linux tools. [13:24:07] Found bwa - /usr/local/bin/bwa [13:24:07] Found bcftools - /usr/local/bin/bcftools [13:24:07] Found samtools - /usr/local/bin/samtools [13:24:07] Found java - /usr/local/bin/java [13:24:07] Found snpEff - /usr/local/bin/snpEff [13:24:07] Found samclip - /usr/local/bin/samclip [13:24:07] Found seqtk - /usr/local/bin/seqtk [13:24:07] Found parallel - /usr/local/bin/parallel [13:24:07] Found freebayes - /usr/local/bin/freebayes [13:24:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [13:24:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [13:24:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [13:24:07] Found vcfuniq - /usr/local/bin/vcfuniq [13:24:07] Found vcffirstheader - /usr/local/bin/vcffirstheader [13:24:07] Found gzip - /bin/gzip [13:24:07] Found vt - /usr/local/bin/vt [13:24:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [13:24:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [13:24:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [13:24:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [13:24:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [13:24:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [13:24:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [13:24:08] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:51:42] This is snippy 4.6.0
Show full stderr[12:51:42] This is snippy 4.6.0 [12:51:42] Written by Torsten Seemann [12:51:42] Obtained from https://github.com/tseemann/snippy [12:51:42] Detected operating system: linux [12:51:42] Enabling bundled linux tools. [12:51:42] Found bwa - /usr/local/bin/bwa [12:51:42] Found bcftools - /usr/local/bin/bcftools [12:51:42] Found samtools - /usr/local/bin/samtools [12:51:42] Found java - /usr/local/bin/java [12:51:42] Found snpEff - /usr/local/bin/snpEff [12:51:42] Found samclip - /usr/local/bin/samclip [12:51:42] Found seqtk - /usr/local/bin/seqtk [12:51:42] Found parallel - /usr/local/bin/parallel [12:51:42] Found freebayes - /usr/local/bin/freebayes [12:51:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:51:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:51:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:51:42] Found vcfuniq - /usr/local/bin/vcfuniq [12:51:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:51:42] Found gzip - /bin/gzip [12:51:42] Found vt - /usr/local/bin/vt [12:51:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:51:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:51:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:51:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:51:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:51:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:51:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:51:43] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:57:37] This is snippy 4.6.0
Show full stderr[12:57:37] This is snippy 4.6.0 [12:57:37] Written by Torsten Seemann [12:57:37] Obtained from https://github.com/tseemann/snippy [12:57:37] Detected operating system: linux [12:57:37] Enabling bundled linux tools. [12:57:37] Found bwa - /usr/local/bin/bwa [12:57:37] Found bcftools - /usr/local/bin/bcftools [12:57:37] Found samtools - /usr/local/bin/samtools [12:57:37] Found java - /usr/local/bin/java [12:57:37] Found snpEff - /usr/local/bin/snpEff [12:57:37] Found samclip - /usr/local/bin/samclip [12:57:37] Found seqtk - /usr/local/bin/seqtk [12:57:37] Found parallel - /usr/local/bin/parallel [12:57:37] Found freebayes - /usr/local/bin/freebayes [12:57:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:57:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:57:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:57:37] Found vcfuniq - /usr/local/bin/vcfuniq [12:57:37] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:57:37] Found gzip - /bin/gzip [12:57:37] Found vt - /usr/local/bin/vt [12:57:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:57:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:57:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:57:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:57:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:57:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:57:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:57:38] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:57:54] This is snippy 4.6.0
Show full stderr[12:57:54] This is snippy 4.6.0 [12:57:54] Written by Torsten Seemann [12:57:54] Obtained from https://github.com/tseemann/snippy [12:57:54] Detected operating system: linux [12:57:54] Enabling bundled linux tools. [12:57:54] Found bwa - /usr/local/bin/bwa [12:57:54] Found bcftools - /usr/local/bin/bcftools [12:57:54] Found samtools - /usr/local/bin/samtools [12:57:54] Found java - /usr/local/bin/java [12:57:54] Found snpEff - /usr/local/bin/snpEff [12:57:54] Found samclip - /usr/local/bin/samclip [12:57:54] Found seqtk - /usr/local/bin/seqtk [12:57:54] Found parallel - /usr/local/bin/parallel [12:57:54] Found freebayes - /usr/local/bin/freebayes [12:57:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:57:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:57:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:57:54] Found vcfuniq - /usr/local/bin/vcfuniq [12:57:55] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:57:55] Found gzip - /bin/gzip [12:57:55] Found vt - /usr/local/bin/vt [12:57:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:57:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:57:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:57:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:57:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:57:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:57:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:57:55] Please supply a reference FASTA/GBK/EMBL file with --reference
1[13:03:54] This is snippy 4.6.0
Show full stderr[13:03:54] This is snippy 4.6.0 [13:03:54] Written by Torsten Seemann [13:03:54] Obtained from https://github.com/tseemann/snippy [13:03:54] Detected operating system: linux [13:03:54] Enabling bundled linux tools. [13:03:54] Found bwa - /usr/local/bin/bwa [13:03:54] Found bcftools - /usr/local/bin/bcftools [13:03:54] Found samtools - /usr/local/bin/samtools [13:03:54] Found java - /usr/local/bin/java [13:03:54] Found snpEff - /usr/local/bin/snpEff [13:03:54] Found samclip - /usr/local/bin/samclip [13:03:54] Found seqtk - /usr/local/bin/seqtk [13:03:54] Found parallel - /usr/local/bin/parallel [13:03:54] Found freebayes - /usr/local/bin/freebayes [13:03:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [13:03:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [13:03:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [13:03:54] Found vcfuniq - /usr/local/bin/vcfuniq [13:03:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [13:03:54] Found gzip - /bin/gzip [13:03:54] Found vt - /usr/local/bin/vt [13:03:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [13:03:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [13:03:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [13:03:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [13:03:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [13:03:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [13:03:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [13:03:58] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:51:18] This is snippy 4.6.0
Show full stderr[12:51:18] This is snippy 4.6.0 [12:51:18] Written by Torsten Seemann [12:51:18] Obtained from https://github.com/tseemann/snippy [12:51:18] Detected operating system: linux [12:51:18] Enabling bundled linux tools. [12:51:18] Found bwa - /usr/local/bin/bwa [12:51:18] Found bcftools - /usr/local/bin/bcftools [12:51:18] Found samtools - /usr/local/bin/samtools [12:51:18] Found java - /usr/local/bin/java [12:51:18] Found snpEff - /usr/local/bin/snpEff [12:51:18] Found samclip - /usr/local/bin/samclip [12:51:18] Found seqtk - /usr/local/bin/seqtk [12:51:18] Found parallel - /usr/local/bin/parallel [12:51:18] Found freebayes - /usr/local/bin/freebayes [12:51:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:51:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:51:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:51:18] Found vcfuniq - /usr/local/bin/vcfuniq [12:51:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:51:18] Found gzip - /bin/gzip [12:51:18] Found vt - /usr/local/bin/vt [12:51:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:51:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:51:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:51:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:51:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:51:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:51:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:51:19] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:55:36] This is snippy 4.6.0
Show full stderr[12:55:36] This is snippy 4.6.0 [12:55:36] Written by Torsten Seemann [12:55:36] Obtained from https://github.com/tseemann/snippy [12:55:36] Detected operating system: linux [12:55:36] Enabling bundled linux tools. [12:55:36] Found bwa - /usr/local/bin/bwa [12:55:36] Found bcftools - /usr/local/bin/bcftools [12:55:36] Found samtools - /usr/local/bin/samtools [12:55:36] Found java - /usr/local/bin/java [12:55:36] Found snpEff - /usr/local/bin/snpEff [12:55:36] Found samclip - /usr/local/bin/samclip [12:55:36] Found seqtk - /usr/local/bin/seqtk [12:55:36] Found parallel - /usr/local/bin/parallel [12:55:36] Found freebayes - /usr/local/bin/freebayes [12:55:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:55:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:55:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:55:36] Found vcfuniq - /usr/local/bin/vcfuniq [12:55:36] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:55:36] Found gzip - /bin/gzip [12:55:36] Found vt - /usr/local/bin/vt [12:55:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:55:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:55:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:55:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:55:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:55:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:55:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:55:37] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:55:47] This is snippy 4.6.0
Show full stderr[12:55:47] This is snippy 4.6.0 [12:55:47] Written by Torsten Seemann [12:55:47] Obtained from https://github.com/tseemann/snippy [12:55:47] Detected operating system: linux [12:55:47] Enabling bundled linux tools. [12:55:47] Found bwa - /usr/local/bin/bwa [12:55:47] Found bcftools - /usr/local/bin/bcftools [12:55:47] Found samtools - /usr/local/bin/samtools [12:55:47] Found java - /usr/local/bin/java [12:55:48] Found snpEff - /usr/local/bin/snpEff [12:55:48] Found samclip - /usr/local/bin/samclip [12:55:48] Found seqtk - /usr/local/bin/seqtk [12:55:48] Found parallel - /usr/local/bin/parallel [12:55:48] Found freebayes - /usr/local/bin/freebayes [12:55:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:55:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:55:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:55:48] Found vcfuniq - /usr/local/bin/vcfuniq [12:55:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:55:48] Found gzip - /bin/gzip [12:55:48] Found vt - /usr/local/bin/vt [12:55:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:55:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:55:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:55:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:55:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:55:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:55:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:55:48] Please supply a reference FASTA/GBK/EMBL file with --reference
1[13:04:22] This is snippy 4.6.0
Show full stderr[13:04:22] This is snippy 4.6.0 [13:04:22] Written by Torsten Seemann [13:04:22] Obtained from https://github.com/tseemann/snippy [13:04:22] Detected operating system: linux [13:04:22] Enabling bundled linux tools. [13:04:22] Found bwa - /usr/local/bin/bwa [13:04:22] Found bcftools - /usr/local/bin/bcftools [13:04:22] Found samtools - /usr/local/bin/samtools [13:04:22] Found java - /usr/local/bin/java [13:04:22] Found snpEff - /usr/local/bin/snpEff [13:04:22] Found samclip - /usr/local/bin/samclip [13:04:22] Found seqtk - /usr/local/bin/seqtk [13:04:22] Found parallel - /usr/local/bin/parallel [13:04:22] Found freebayes - /usr/local/bin/freebayes [13:04:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [13:04:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [13:04:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [13:04:22] Found vcfuniq - /usr/local/bin/vcfuniq [13:04:22] Found vcffirstheader - /usr/local/bin/vcffirstheader [13:04:22] Found gzip - /bin/gzip [13:04:22] Found vt - /usr/local/bin/vt [13:04:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [13:04:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [13:04:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [13:04:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [13:04:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [13:04:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [13:04:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [13:04:22] Please supply a reference FASTA/GBK/EMBL file with --reference
1[13:10:08] This is snippy 4.6.0
Show full stderr[13:10:08] This is snippy 4.6.0 [13:10:08] Written by Torsten Seemann [13:10:08] Obtained from https://github.com/tseemann/snippy [13:10:08] Detected operating system: linux [13:10:08] Enabling bundled linux tools. [13:10:08] Found bwa - /usr/local/bin/bwa [13:10:08] Found bcftools - /usr/local/bin/bcftools [13:10:08] Found samtools - /usr/local/bin/samtools [13:10:08] Found java - /usr/local/bin/java [13:10:08] Found snpEff - /usr/local/bin/snpEff [13:10:08] Found samclip - /usr/local/bin/samclip [13:10:08] Found seqtk - /usr/local/bin/seqtk [13:10:08] Found parallel - /usr/local/bin/parallel [13:10:08] Found freebayes - /usr/local/bin/freebayes [13:10:08] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [13:10:08] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [13:10:08] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [13:10:08] Found vcfuniq - /usr/local/bin/vcfuniq [13:10:08] Found vcffirstheader - /usr/local/bin/vcffirstheader [13:10:08] Found gzip - /bin/gzip [13:10:08] Found vt - /usr/local/bin/vt [13:10:08] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [13:10:08] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [13:10:08] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [13:10:08] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [13:10:08] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [13:10:09] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [13:10:09] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [13:10:09] Please supply a reference FASTA/GBK/EMBL file with --reference
1[13:16:56] This is snippy 4.6.0
Show full stderr[13:16:56] This is snippy 4.6.0 [13:16:56] Written by Torsten Seemann [13:16:56] Obtained from https://github.com/tseemann/snippy [13:16:56] Detected operating system: linux [13:16:56] Enabling bundled linux tools. [13:16:56] Found bwa - /usr/local/bin/bwa [13:16:56] Found bcftools - /usr/local/bin/bcftools [13:16:56] Found samtools - /usr/local/bin/samtools [13:16:56] Found java - /usr/local/bin/java [13:16:56] Found snpEff - /usr/local/bin/snpEff [13:16:56] Found samclip - /usr/local/bin/samclip [13:16:56] Found seqtk - /usr/local/bin/seqtk [13:16:56] Found parallel - /usr/local/bin/parallel [13:16:56] Found freebayes - /usr/local/bin/freebayes [13:16:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [13:16:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [13:16:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [13:16:56] Found vcfuniq - /usr/local/bin/vcfuniq [13:16:56] Found vcffirstheader - /usr/local/bin/vcffirstheader [13:16:56] Found gzip - /bin/gzip [13:16:56] Found vt - /usr/local/bin/vt [13:16:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [13:16:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [13:16:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [13:16:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [13:16:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [13:16:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [13:16:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [13:16:56] Please supply a reference FASTA/GBK/EMBL file with --reference
1[13:16:47] This is snippy 4.6.0
Show full stderr[13:16:47] This is snippy 4.6.0 [13:16:47] Written by Torsten Seemann [13:16:47] Obtained from https://github.com/tseemann/snippy [13:16:47] Detected operating system: linux [13:16:47] Enabling bundled linux tools. [13:16:47] Found bwa - /usr/local/bin/bwa [13:16:47] Found bcftools - /usr/local/bin/bcftools [13:16:47] Found samtools - /usr/local/bin/samtools [13:16:47] Found java - /usr/local/bin/java [13:16:47] Found snpEff - /usr/local/bin/snpEff [13:16:47] Found samclip - /usr/local/bin/samclip [13:16:47] Found seqtk - /usr/local/bin/seqtk [13:16:47] Found parallel - /usr/local/bin/parallel [13:16:47] Found freebayes - /usr/local/bin/freebayes [13:16:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [13:16:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [13:16:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [13:16:47] Found vcfuniq - /usr/local/bin/vcfuniq [13:16:47] Found vcffirstheader - /usr/local/bin/vcffirstheader [13:16:47] Found gzip - /bin/gzip [13:16:47] Found vt - /usr/local/bin/vt [13:16:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [13:16:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [13:16:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [13:16:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [13:16:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [13:16:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [13:16:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [13:16:48] Please supply a reference FASTA/GBK/EMBL file with --reference
1[13:25:32] This is snippy 4.6.0
Show full stderr[13:25:32] This is snippy 4.6.0 [13:25:32] Written by Torsten Seemann [13:25:32] Obtained from https://github.com/tseemann/snippy [13:25:32] Detected operating system: linux [13:25:32] Enabling bundled linux tools. [13:25:32] Found bwa - /usr/local/bin/bwa [13:25:32] Found bcftools - /usr/local/bin/bcftools [13:25:32] Found samtools - /usr/local/bin/samtools [13:25:32] Found java - /usr/local/bin/java [13:25:32] Found snpEff - /usr/local/bin/snpEff [13:25:32] Found samclip - /usr/local/bin/samclip [13:25:32] Found seqtk - /usr/local/bin/seqtk [13:25:32] Found parallel - /usr/local/bin/parallel [13:25:32] Found freebayes - /usr/local/bin/freebayes [13:25:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [13:25:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [13:25:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [13:25:32] Found vcfuniq - /usr/local/bin/vcfuniq [13:25:32] Found vcffirstheader - /usr/local/bin/vcffirstheader [13:25:32] Found gzip - /bin/gzip [13:25:32] Found vt - /usr/local/bin/vt [13:25:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [13:25:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [13:25:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [13:25:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [13:25:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [13:25:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [13:25:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [13:25:33] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:56:05] This is snippy 4.6.0
Show full stderr[12:56:05] This is snippy 4.6.0 [12:56:05] Written by Torsten Seemann [12:56:05] Obtained from https://github.com/tseemann/snippy [12:56:05] Detected operating system: linux [12:56:05] Enabling bundled linux tools. [12:56:05] Found bwa - /usr/local/bin/bwa [12:56:05] Found bcftools - /usr/local/bin/bcftools [12:56:05] Found samtools - /usr/local/bin/samtools [12:56:05] Found java - /usr/local/bin/java [12:56:05] Found snpEff - /usr/local/bin/snpEff [12:56:05] Found samclip - /usr/local/bin/samclip [12:56:05] Found seqtk - /usr/local/bin/seqtk [12:56:05] Found parallel - /usr/local/bin/parallel [12:56:05] Found freebayes - /usr/local/bin/freebayes [12:56:05] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:56:05] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:56:05] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:56:05] Found vcfuniq - /usr/local/bin/vcfuniq [12:56:05] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:56:05] Found gzip - /bin/gzip [12:56:05] Found vt - /usr/local/bin/vt [12:56:05] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:56:05] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:56:05] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:56:05] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:56:05] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:56:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:56:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:56:06] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:56:14] This is snippy 4.6.0
Show full stderr[12:56:14] This is snippy 4.6.0 [12:56:14] Written by Torsten Seemann [12:56:14] Obtained from https://github.com/tseemann/snippy [12:56:14] Detected operating system: linux [12:56:14] Enabling bundled linux tools. [12:56:14] Found bwa - /usr/local/bin/bwa [12:56:14] Found bcftools - /usr/local/bin/bcftools [12:56:14] Found samtools - /usr/local/bin/samtools [12:56:14] Found java - /usr/local/bin/java [12:56:14] Found snpEff - /usr/local/bin/snpEff [12:56:14] Found samclip - /usr/local/bin/samclip [12:56:14] Found seqtk - /usr/local/bin/seqtk [12:56:14] Found parallel - /usr/local/bin/parallel [12:56:14] Found freebayes - /usr/local/bin/freebayes [12:56:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:56:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:56:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:56:14] Found vcfuniq - /usr/local/bin/vcfuniq [12:56:14] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:56:14] Found gzip - /bin/gzip [12:56:14] Found vt - /usr/local/bin/vt [12:56:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:56:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:56:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:56:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:56:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:56:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:56:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:56:14] Please supply a reference FASTA/GBK/EMBL file with --reference
1[13:25:49] This is snippy 4.6.0
Show full stderr[13:25:49] This is snippy 4.6.0 [13:25:49] Written by Torsten Seemann [13:25:49] Obtained from https://github.com/tseemann/snippy [13:25:49] Detected operating system: linux [13:25:49] Enabling bundled linux tools. [13:25:49] Found bwa - /usr/local/bin/bwa [13:25:49] Found bcftools - /usr/local/bin/bcftools [13:25:49] Found samtools - /usr/local/bin/samtools [13:25:49] Found java - /usr/local/bin/java [13:25:49] Found snpEff - /usr/local/bin/snpEff [13:25:49] Found samclip - /usr/local/bin/samclip [13:25:49] Found seqtk - /usr/local/bin/seqtk [13:25:49] Found parallel - /usr/local/bin/parallel [13:25:49] Found freebayes - /usr/local/bin/freebayes [13:25:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [13:25:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [13:25:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [13:25:49] Found vcfuniq - /usr/local/bin/vcfuniq [13:25:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [13:25:49] Found gzip - /bin/gzip [13:25:49] Found vt - /usr/local/bin/vt [13:25:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [13:25:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [13:25:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [13:25:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [13:25:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [13:25:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [13:25:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [13:25:50] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:56:11] This is snippy 4.6.0
Show full stderr[12:56:11] This is snippy 4.6.0 [12:56:11] Written by Torsten Seemann [12:56:11] Obtained from https://github.com/tseemann/snippy [12:56:11] Detected operating system: linux [12:56:11] Enabling bundled linux tools. [12:56:11] Found bwa - /usr/local/bin/bwa [12:56:11] Found bcftools - /usr/local/bin/bcftools [12:56:11] Found samtools - /usr/local/bin/samtools [12:56:11] Found java - /usr/local/bin/java [12:56:11] Found snpEff - /usr/local/bin/snpEff [12:56:11] Found samclip - /usr/local/bin/samclip [12:56:11] Found seqtk - /usr/local/bin/seqtk [12:56:11] Found parallel - /usr/local/bin/parallel [12:56:11] Found freebayes - /usr/local/bin/freebayes [12:56:11] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:56:11] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:56:11] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:56:11] Found vcfuniq - /usr/local/bin/vcfuniq [12:56:11] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:56:11] Found gzip - /bin/gzip [12:56:11] Found vt - /usr/local/bin/vt [12:56:11] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:56:11] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:56:11] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:56:11] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:56:11] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:56:12] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:56:12] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:56:12] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:56:17] This is snippy 4.6.0
Show full stderr[12:56:17] This is snippy 4.6.0 [12:56:17] Written by Torsten Seemann [12:56:17] Obtained from https://github.com/tseemann/snippy [12:56:17] Detected operating system: linux [12:56:17] Enabling bundled linux tools. [12:56:17] Found bwa - /usr/local/bin/bwa [12:56:17] Found bcftools - /usr/local/bin/bcftools [12:56:17] Found samtools - /usr/local/bin/samtools [12:56:17] Found java - /usr/local/bin/java [12:56:17] Found snpEff - /usr/local/bin/snpEff [12:56:17] Found samclip - /usr/local/bin/samclip [12:56:17] Found seqtk - /usr/local/bin/seqtk [12:56:17] Found parallel - /usr/local/bin/parallel [12:56:17] Found freebayes - /usr/local/bin/freebayes [12:56:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:56:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:56:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:56:17] Found vcfuniq - /usr/local/bin/vcfuniq [12:56:17] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:56:17] Found gzip - /bin/gzip [12:56:17] Found vt - /usr/local/bin/vt [12:56:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:56:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:56:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:56:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:56:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:56:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:56:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:56:18] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:56:35] This is snippy 4.6.0
Show full stderr[12:56:35] This is snippy 4.6.0 [12:56:35] Written by Torsten Seemann [12:56:35] Obtained from https://github.com/tseemann/snippy [12:56:35] Detected operating system: linux [12:56:35] Enabling bundled linux tools. [12:56:35] Found bwa - /usr/local/bin/bwa [12:56:35] Found bcftools - /usr/local/bin/bcftools [12:56:35] Found samtools - /usr/local/bin/samtools [12:56:35] Found java - /usr/local/bin/java [12:56:35] Found snpEff - /usr/local/bin/snpEff [12:56:35] Found samclip - /usr/local/bin/samclip [12:56:35] Found seqtk - /usr/local/bin/seqtk [12:56:35] Found parallel - /usr/local/bin/parallel [12:56:35] Found freebayes - /usr/local/bin/freebayes [12:56:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:56:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:56:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:56:35] Found vcfuniq - /usr/local/bin/vcfuniq [12:56:35] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:56:35] Found gzip - /bin/gzip [12:56:35] Found vt - /usr/local/bin/vt [12:56:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:56:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:56:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:56:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:56:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:56:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:56:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:56:35] Please supply a reference FASTA/GBK/EMBL file with --reference
1[13:24:32] This is snippy 4.6.0
Show full stderr[13:24:32] This is snippy 4.6.0 [13:24:32] Written by Torsten Seemann [13:24:32] Obtained from https://github.com/tseemann/snippy [13:24:32] Detected operating system: linux [13:24:32] Enabling bundled linux tools. [13:24:32] Found bwa - /usr/local/bin/bwa [13:24:32] Found bcftools - /usr/local/bin/bcftools [13:24:32] Found samtools - /usr/local/bin/samtools [13:24:32] Found java - /usr/local/bin/java [13:24:32] Found snpEff - /usr/local/bin/snpEff [13:24:32] Found samclip - /usr/local/bin/samclip [13:24:32] Found seqtk - /usr/local/bin/seqtk [13:24:32] Found parallel - /usr/local/bin/parallel [13:24:32] Found freebayes - /usr/local/bin/freebayes [13:24:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [13:24:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [13:24:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [13:24:32] Found vcfuniq - /usr/local/bin/vcfuniq [13:24:32] Found vcffirstheader - /usr/local/bin/vcffirstheader [13:24:32] Found gzip - /bin/gzip [13:24:32] Found vt - /usr/local/bin/vt [13:24:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [13:24:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [13:24:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [13:24:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [13:24:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [13:24:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [13:24:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [13:24:33] Please supply a reference FASTA/GBK/EMBL file with --reference
1[13:30:25] This is snippy 4.6.0
Show full stderr[13:30:25] This is snippy 4.6.0 [13:30:25] Written by Torsten Seemann [13:30:25] Obtained from https://github.com/tseemann/snippy [13:30:25] Detected operating system: linux [13:30:25] Enabling bundled linux tools. [13:30:25] Found bwa - /usr/local/bin/bwa [13:30:25] Found bcftools - /usr/local/bin/bcftools [13:30:25] Found samtools - /usr/local/bin/samtools [13:30:25] Found java - /usr/local/bin/java [13:30:25] Found snpEff - /usr/local/bin/snpEff [13:30:25] Found samclip - /usr/local/bin/samclip [13:30:25] Found seqtk - /usr/local/bin/seqtk [13:30:25] Found parallel - /usr/local/bin/parallel [13:30:25] Found freebayes - /usr/local/bin/freebayes [13:30:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [13:30:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [13:30:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [13:30:26] Found vcfuniq - /usr/local/bin/vcfuniq [13:30:26] Found vcffirstheader - /usr/local/bin/vcffirstheader [13:30:26] Found gzip - /bin/gzip [13:30:26] Found vt - /usr/local/bin/vt [13:30:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [13:30:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [13:30:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [13:30:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [13:30:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [13:30:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [13:30:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [13:30:28] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:56:38] This is snippy 4.6.0
Show full stderr[12:56:38] This is snippy 4.6.0 [12:56:38] Written by Torsten Seemann [12:56:38] Obtained from https://github.com/tseemann/snippy [12:56:38] Detected operating system: linux [12:56:38] Enabling bundled linux tools. [12:56:38] Found bwa - /usr/local/bin/bwa [12:56:38] Found bcftools - /usr/local/bin/bcftools [12:56:38] Found samtools - /usr/local/bin/samtools [12:56:38] Found java - /usr/local/bin/java [12:56:38] Found snpEff - /usr/local/bin/snpEff [12:56:38] Found samclip - /usr/local/bin/samclip [12:56:38] Found seqtk - /usr/local/bin/seqtk [12:56:38] Found parallel - /usr/local/bin/parallel [12:56:38] Found freebayes - /usr/local/bin/freebayes [12:56:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:56:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:56:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:56:38] Found vcfuniq - /usr/local/bin/vcfuniq [12:56:38] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:56:38] Found gzip - /bin/gzip [12:56:38] Found vt - /usr/local/bin/vt [12:56:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:56:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:56:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:56:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:56:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:56:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:56:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:56:38] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:56:50] This is snippy 4.6.0
Show full stderr[12:56:50] This is snippy 4.6.0 [12:56:50] Written by Torsten Seemann [12:56:50] Obtained from https://github.com/tseemann/snippy [12:56:50] Detected operating system: linux [12:56:50] Enabling bundled linux tools. [12:56:50] Found bwa - /usr/local/bin/bwa [12:56:50] Found bcftools - /usr/local/bin/bcftools [12:56:50] Found samtools - /usr/local/bin/samtools [12:56:50] Found java - /usr/local/bin/java [12:56:50] Found snpEff - /usr/local/bin/snpEff [12:56:50] Found samclip - /usr/local/bin/samclip [12:56:50] Found seqtk - /usr/local/bin/seqtk [12:56:50] Found parallel - /usr/local/bin/parallel [12:56:50] Found freebayes - /usr/local/bin/freebayes [12:56:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:56:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:56:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:56:50] Found vcfuniq - /usr/local/bin/vcfuniq [12:56:50] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:56:50] Found gzip - /bin/gzip [12:56:50] Found vt - /usr/local/bin/vt [12:56:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:56:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:56:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:56:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:56:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:56:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:56:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:56:50] Please supply a reference FASTA/GBK/EMBL file with --reference
1[13:32:09] This is snippy 4.6.0
Show full stderr[13:32:09] This is snippy 4.6.0 [13:32:09] Written by Torsten Seemann [13:32:09] Obtained from https://github.com/tseemann/snippy [13:32:09] Detected operating system: linux [13:32:09] Enabling bundled linux tools. [13:32:09] Found bwa - /usr/local/bin/bwa [13:32:09] Found bcftools - /usr/local/bin/bcftools [13:32:09] Found samtools - /usr/local/bin/samtools [13:32:09] Found java - /usr/local/bin/java [13:32:09] Found snpEff - /usr/local/bin/snpEff [13:32:09] Found samclip - /usr/local/bin/samclip [13:32:09] Found seqtk - /usr/local/bin/seqtk [13:32:09] Found parallel - /usr/local/bin/parallel [13:32:09] Found freebayes - /usr/local/bin/freebayes [13:32:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [13:32:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [13:32:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [13:32:09] Found vcfuniq - /usr/local/bin/vcfuniq [13:32:09] Found vcffirstheader - /usr/local/bin/vcffirstheader [13:32:09] Found gzip - /bin/gzip [13:32:09] Found vt - /usr/local/bin/vt [13:32:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [13:32:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [13:32:11] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [13:32:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [13:32:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [13:32:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [13:32:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [13:32:15] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:56:56] This is snippy 4.6.0
Show full stderr[12:56:56] This is snippy 4.6.0 [12:56:56] Written by Torsten Seemann [12:56:56] Obtained from https://github.com/tseemann/snippy [12:56:56] Detected operating system: linux [12:56:56] Enabling bundled linux tools. [12:56:56] Found bwa - /usr/local/bin/bwa [12:56:56] Found bcftools - /usr/local/bin/bcftools [12:56:56] Found samtools - /usr/local/bin/samtools [12:56:56] Found java - /usr/local/bin/java [12:56:56] Found snpEff - /usr/local/bin/snpEff [12:56:56] Found samclip - /usr/local/bin/samclip [12:56:56] Found seqtk - /usr/local/bin/seqtk [12:56:56] Found parallel - /usr/local/bin/parallel [12:56:56] Found freebayes - /usr/local/bin/freebayes [12:56:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:56:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:56:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:56:56] Found vcfuniq - /usr/local/bin/vcfuniq [12:56:56] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:56:56] Found gzip - /bin/gzip [12:56:56] Found vt - /usr/local/bin/vt [12:56:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:56:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:56:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:56:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:56:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:56:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:56:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:56:57] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:57:23] This is snippy 4.6.0
Show full stderr[12:57:23] This is snippy 4.6.0 [12:57:23] Written by Torsten Seemann [12:57:23] Obtained from https://github.com/tseemann/snippy [12:57:23] Detected operating system: linux [12:57:23] Enabling bundled linux tools. [12:57:23] Found bwa - /usr/local/bin/bwa [12:57:23] Found bcftools - /usr/local/bin/bcftools [12:57:23] Found samtools - /usr/local/bin/samtools [12:57:23] Found java - /usr/local/bin/java [12:57:23] Found snpEff - /usr/local/bin/snpEff [12:57:23] Found samclip - /usr/local/bin/samclip [12:57:23] Found seqtk - /usr/local/bin/seqtk [12:57:23] Found parallel - /usr/local/bin/parallel [12:57:23] Found freebayes - /usr/local/bin/freebayes [12:57:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:57:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:57:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:57:23] Found vcfuniq - /usr/local/bin/vcfuniq [12:57:23] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:57:23] Found gzip - /bin/gzip [12:57:23] Found vt - /usr/local/bin/vt [12:57:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:57:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:57:23] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:57:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:57:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:57:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:57:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:57:24] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:57:30] This is snippy 4.6.0
Show full stderr[12:57:30] This is snippy 4.6.0 [12:57:30] Written by Torsten Seemann [12:57:30] Obtained from https://github.com/tseemann/snippy [12:57:30] Detected operating system: linux [12:57:30] Enabling bundled linux tools. [12:57:30] Found bwa - /usr/local/bin/bwa [12:57:30] Found bcftools - /usr/local/bin/bcftools [12:57:30] Found samtools - /usr/local/bin/samtools [12:57:30] Found java - /usr/local/bin/java [12:57:30] Found snpEff - /usr/local/bin/snpEff [12:57:30] Found samclip - /usr/local/bin/samclip [12:57:30] Found seqtk - /usr/local/bin/seqtk [12:57:30] Found parallel - /usr/local/bin/parallel [12:57:30] Found freebayes - /usr/local/bin/freebayes [12:57:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:57:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:57:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:57:30] Found vcfuniq - /usr/local/bin/vcfuniq [12:57:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:57:30] Found gzip - /bin/gzip [12:57:30] Found vt - /usr/local/bin/vt [12:57:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:57:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:57:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:57:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:57:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:57:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:57:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:57:31] Please supply a reference FASTA/GBK/EMBL file with --reference
1[13:33:00] This is snippy 4.6.0
Show full stderr[13:33:00] This is snippy 4.6.0 [13:33:00] Written by Torsten Seemann [13:33:00] Obtained from https://github.com/tseemann/snippy [13:33:00] Detected operating system: linux [13:33:00] Enabling bundled linux tools. [13:33:00] Found bwa - /usr/local/bin/bwa [13:33:00] Found bcftools - /usr/local/bin/bcftools [13:33:00] Found samtools - /usr/local/bin/samtools [13:33:00] Found java - /usr/local/bin/java [13:33:00] Found snpEff - /usr/local/bin/snpEff [13:33:00] Found samclip - /usr/local/bin/samclip [13:33:00] Found seqtk - /usr/local/bin/seqtk [13:33:00] Found parallel - /usr/local/bin/parallel [13:33:00] Found freebayes - /usr/local/bin/freebayes [13:33:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [13:33:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [13:33:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [13:33:00] Found vcfuniq - /usr/local/bin/vcfuniq [13:33:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [13:33:00] Found gzip - /bin/gzip [13:33:00] Found vt - /usr/local/bin/vt [13:33:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [13:33:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [13:33:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [13:33:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [13:33:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [13:33:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [13:33:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [13:33:01] Please supply a reference FASTA/GBK/EMBL file with --reference
1[13:04:45] This is snippy 4.6.0
Show full stderr[13:04:45] This is snippy 4.6.0 [13:04:45] Written by Torsten Seemann [13:04:45] Obtained from https://github.com/tseemann/snippy [13:04:45] Detected operating system: linux [13:04:45] Enabling bundled linux tools. [13:04:45] Found bwa - /usr/local/bin/bwa [13:04:45] Found bcftools - /usr/local/bin/bcftools [13:04:45] Found samtools - /usr/local/bin/samtools [13:04:45] Found java - /usr/local/bin/java [13:04:45] Found snpEff - /usr/local/bin/snpEff [13:04:45] Found samclip - /usr/local/bin/samclip [13:04:45] Found seqtk - /usr/local/bin/seqtk [13:04:45] Found parallel - /usr/local/bin/parallel [13:04:45] Found freebayes - /usr/local/bin/freebayes [13:04:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [13:04:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [13:04:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [13:04:45] Found vcfuniq - /usr/local/bin/vcfuniq [13:04:45] Found vcffirstheader - /usr/local/bin/vcffirstheader [13:04:45] Found gzip - /bin/gzip [13:04:45] Found vt - /usr/local/bin/vt [13:04:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [13:04:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [13:04:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [13:04:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [13:04:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [13:04:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [13:04:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [13:04:46] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:51:33] This is snippy 4.6.0
Show full stderr[12:51:33] This is snippy 4.6.0 [12:51:33] Written by Torsten Seemann [12:51:33] Obtained from https://github.com/tseemann/snippy [12:51:33] Detected operating system: linux [12:51:33] Enabling bundled linux tools. [12:51:33] Found bwa - /usr/local/bin/bwa [12:51:33] Found bcftools - /usr/local/bin/bcftools [12:51:33] Found samtools - /usr/local/bin/samtools [12:51:33] Found java - /usr/local/bin/java [12:51:33] Found snpEff - /usr/local/bin/snpEff [12:51:33] Found samclip - /usr/local/bin/samclip [12:51:33] Found seqtk - /usr/local/bin/seqtk [12:51:33] Found parallel - /usr/local/bin/parallel [12:51:33] Found freebayes - /usr/local/bin/freebayes [12:51:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:51:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:51:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:51:33] Found vcfuniq - /usr/local/bin/vcfuniq [12:51:33] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:51:33] Found gzip - /bin/gzip [12:51:33] Found vt - /usr/local/bin/vt [12:51:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:51:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:51:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:51:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:51:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:51:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:51:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:51:34] Please supply a reference FASTA/GBK/EMBL file with --reference
1[13:11:21] This is snippy 4.6.0
Show full stderr[13:11:21] This is snippy 4.6.0 [13:11:21] Written by Torsten Seemann [13:11:21] Obtained from https://github.com/tseemann/snippy [13:11:21] Detected operating system: linux [13:11:21] Enabling bundled linux tools. [13:11:21] Found bwa - /usr/local/bin/bwa [13:11:21] Found bcftools - /usr/local/bin/bcftools [13:11:21] Found samtools - /usr/local/bin/samtools [13:11:21] Found java - /usr/local/bin/java [13:11:21] Found snpEff - /usr/local/bin/snpEff [13:11:21] Found samclip - /usr/local/bin/samclip [13:11:21] Found seqtk - /usr/local/bin/seqtk [13:11:21] Found parallel - /usr/local/bin/parallel [13:11:21] Found freebayes - /usr/local/bin/freebayes [13:11:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [13:11:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [13:11:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [13:11:21] Found vcfuniq - /usr/local/bin/vcfuniq [13:11:21] Found vcffirstheader - /usr/local/bin/vcffirstheader [13:11:21] Found gzip - /bin/gzip [13:11:21] Found vt - /usr/local/bin/vt [13:11:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [13:11:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [13:11:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [13:11:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [13:11:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [13:11:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [13:11:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [13:11:22] Please supply a reference FASTA/GBK/EMBL file with --reference
1[13:17:15] This is snippy 4.6.0
Show full stderr[13:17:15] This is snippy 4.6.0 [13:17:15] Written by Torsten Seemann [13:17:15] Obtained from https://github.com/tseemann/snippy [13:17:15] Detected operating system: linux [13:17:15] Enabling bundled linux tools. [13:17:15] Found bwa - /usr/local/bin/bwa [13:17:15] Found bcftools - /usr/local/bin/bcftools [13:17:15] Found samtools - /usr/local/bin/samtools [13:17:15] Found java - /usr/local/bin/java [13:17:15] Found snpEff - /usr/local/bin/snpEff [13:17:15] Found samclip - /usr/local/bin/samclip [13:17:15] Found seqtk - /usr/local/bin/seqtk [13:17:15] Found parallel - /usr/local/bin/parallel [13:17:15] Found freebayes - /usr/local/bin/freebayes [13:17:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [13:17:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [13:17:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [13:17:15] Found vcfuniq - /usr/local/bin/vcfuniq [13:17:15] Found vcffirstheader - /usr/local/bin/vcffirstheader [13:17:15] Found gzip - /bin/gzip [13:17:15] Found vt - /usr/local/bin/vt [13:17:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [13:17:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [13:17:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [13:17:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [13:17:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [13:17:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [13:17:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [13:17:16] Please supply a reference FASTA/GBK/EMBL file with --reference
1[13:16:55] This is snippy 4.6.0
Show full stderr[13:16:55] This is snippy 4.6.0 [13:16:55] Written by Torsten Seemann [13:16:55] Obtained from https://github.com/tseemann/snippy [13:16:55] Detected operating system: linux [13:16:55] Enabling bundled linux tools. [13:16:55] Found bwa - /usr/local/bin/bwa [13:16:55] Found bcftools - /usr/local/bin/bcftools [13:16:55] Found samtools - /usr/local/bin/samtools [13:16:55] Found java - /usr/local/bin/java [13:16:55] Found snpEff - /usr/local/bin/snpEff [13:16:55] Found samclip - /usr/local/bin/samclip [13:16:55] Found seqtk - /usr/local/bin/seqtk [13:16:55] Found parallel - /usr/local/bin/parallel [13:16:55] Found freebayes - /usr/local/bin/freebayes [13:16:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [13:16:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [13:16:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [13:16:55] Found vcfuniq - /usr/local/bin/vcfuniq [13:16:55] Found vcffirstheader - /usr/local/bin/vcffirstheader [13:16:55] Found gzip - /bin/gzip [13:16:55] Found vt - /usr/local/bin/vt [13:16:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [13:16:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [13:16:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [13:16:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [13:16:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [13:17:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [13:17:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [13:17:02] Please supply a reference FASTA/GBK/EMBL file with --reference
1[13:16:50] This is snippy 4.6.0
Show full stderr[13:16:50] This is snippy 4.6.0 [13:16:50] Written by Torsten Seemann [13:16:50] Obtained from https://github.com/tseemann/snippy [13:16:50] Detected operating system: linux [13:16:50] Enabling bundled linux tools. [13:16:50] Found bwa - /usr/local/bin/bwa [13:16:50] Found bcftools - /usr/local/bin/bcftools [13:16:50] Found samtools - /usr/local/bin/samtools [13:16:50] Found java - /usr/local/bin/java [13:16:50] Found snpEff - /usr/local/bin/snpEff [13:16:50] Found samclip - /usr/local/bin/samclip [13:16:50] Found seqtk - /usr/local/bin/seqtk [13:16:50] Found parallel - /usr/local/bin/parallel [13:16:50] Found freebayes - /usr/local/bin/freebayes [13:16:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [13:16:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [13:16:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [13:16:50] Found vcfuniq - /usr/local/bin/vcfuniq [13:16:50] Found vcffirstheader - /usr/local/bin/vcffirstheader [13:16:50] Found gzip - /bin/gzip [13:16:50] Found vt - /usr/local/bin/vt [13:16:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [13:16:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [13:16:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [13:16:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [13:16:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [13:16:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [13:16:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [13:16:51] Please supply a reference FASTA/GBK/EMBL file with --reference
1[13:17:56] This is snippy 4.6.0
Show full stderr[13:17:56] This is snippy 4.6.0 [13:17:56] Written by Torsten Seemann [13:17:56] Obtained from https://github.com/tseemann/snippy [13:17:56] Detected operating system: linux [13:17:56] Enabling bundled linux tools. [13:17:56] Found bwa - /usr/local/bin/bwa [13:17:56] Found bcftools - /usr/local/bin/bcftools [13:17:56] Found samtools - /usr/local/bin/samtools [13:17:56] Found java - /usr/local/bin/java [13:17:56] Found snpEff - /usr/local/bin/snpEff [13:17:56] Found samclip - /usr/local/bin/samclip [13:17:56] Found seqtk - /usr/local/bin/seqtk [13:17:56] Found parallel - /usr/local/bin/parallel [13:17:56] Found freebayes - /usr/local/bin/freebayes [13:17:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [13:17:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [13:17:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [13:17:56] Found vcfuniq - /usr/local/bin/vcfuniq [13:17:56] Found vcffirstheader - /usr/local/bin/vcffirstheader [13:17:56] Found gzip - /bin/gzip [13:17:56] Found vt - /usr/local/bin/vt [13:17:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [13:17:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [13:17:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [13:17:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [13:17:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [13:17:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [13:17:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [13:17:59] Please supply a reference FASTA/GBK/EMBL file with --reference
1[13:25:02] This is snippy 4.6.0
Show full stderr[13:25:02] This is snippy 4.6.0 [13:25:02] Written by Torsten Seemann [13:25:02] Obtained from https://github.com/tseemann/snippy [13:25:02] Detected operating system: linux [13:25:02] Enabling bundled linux tools. [13:25:02] Found bwa - /usr/local/bin/bwa [13:25:02] Found bcftools - /usr/local/bin/bcftools [13:25:02] Found samtools - /usr/local/bin/samtools [13:25:02] Found java - /usr/local/bin/java [13:25:02] Found snpEff - /usr/local/bin/snpEff [13:25:02] Found samclip - /usr/local/bin/samclip [13:25:02] Found seqtk - /usr/local/bin/seqtk [13:25:02] Found parallel - /usr/local/bin/parallel [13:25:02] Found freebayes - /usr/local/bin/freebayes [13:25:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [13:25:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [13:25:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [13:25:02] Found vcfuniq - /usr/local/bin/vcfuniq [13:25:02] Found vcffirstheader - /usr/local/bin/vcffirstheader [13:25:02] Found gzip - /bin/gzip [13:25:02] Found vt - /usr/local/bin/vt [13:25:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [13:25:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [13:25:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [13:25:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [13:25:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [13:25:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [13:25:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [13:25:03] Please supply a reference FASTA/GBK/EMBL file with --reference
1[13:18:06] This is snippy 4.6.0
Show full stderr[13:18:06] This is snippy 4.6.0 [13:18:06] Written by Torsten Seemann [13:18:06] Obtained from https://github.com/tseemann/snippy [13:18:06] Detected operating system: linux [13:18:06] Enabling bundled linux tools. [13:18:06] Found bwa - /usr/local/bin/bwa [13:18:06] Found bcftools - /usr/local/bin/bcftools [13:18:06] Found samtools - /usr/local/bin/samtools [13:18:06] Found java - /usr/local/bin/java [13:18:06] Found snpEff - /usr/local/bin/snpEff [13:18:06] Found samclip - /usr/local/bin/samclip [13:18:06] Found seqtk - /usr/local/bin/seqtk [13:18:06] Found parallel - /usr/local/bin/parallel [13:18:06] Found freebayes - /usr/local/bin/freebayes [13:18:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [13:18:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [13:18:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [13:18:06] Found vcfuniq - /usr/local/bin/vcfuniq [13:18:06] Found vcffirstheader - /usr/local/bin/vcffirstheader [13:18:06] Found gzip - /bin/gzip [13:18:06] Found vt - /usr/local/bin/vt [13:18:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [13:18:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [13:18:08] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [13:18:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [13:18:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [13:18:12] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [13:18:12] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [13:18:12] Please supply a reference FASTA/GBK/EMBL file with --reference
1[13:23:54] This is snippy 4.6.0
Show full stderr[13:23:54] This is snippy 4.6.0 [13:23:54] Written by Torsten Seemann [13:23:54] Obtained from https://github.com/tseemann/snippy [13:23:54] Detected operating system: linux [13:23:54] Enabling bundled linux tools. [13:23:54] Found bwa - /usr/local/bin/bwa [13:23:54] Found bcftools - /usr/local/bin/bcftools [13:23:54] Found samtools - /usr/local/bin/samtools [13:23:54] Found java - /usr/local/bin/java [13:23:54] Found snpEff - /usr/local/bin/snpEff [13:23:54] Found samclip - /usr/local/bin/samclip [13:23:54] Found seqtk - /usr/local/bin/seqtk [13:23:54] Found parallel - /usr/local/bin/parallel [13:23:54] Found freebayes - /usr/local/bin/freebayes [13:23:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [13:23:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [13:23:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [13:23:54] Found vcfuniq - /usr/local/bin/vcfuniq [13:23:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [13:23:54] Found gzip - /bin/gzip [13:23:54] Found vt - /usr/local/bin/vt [13:23:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [13:23:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [13:23:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [13:23:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [13:23:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [13:24:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [13:24:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [13:24:00] Please supply a reference FASTA/GBK/EMBL file with --reference
1[13:04:08] This is snippy 4.6.0
Show full stderr[13:04:08] This is snippy 4.6.0 [13:04:08] Written by Torsten Seemann [13:04:08] Obtained from https://github.com/tseemann/snippy [13:04:08] Detected operating system: linux [13:04:08] Enabling bundled linux tools. [13:04:08] Found bwa - /usr/local/bin/bwa [13:04:08] Found bcftools - /usr/local/bin/bcftools [13:04:08] Found samtools - /usr/local/bin/samtools [13:04:08] Found java - /usr/local/bin/java [13:04:08] Found snpEff - /usr/local/bin/snpEff [13:04:08] Found samclip - /usr/local/bin/samclip [13:04:08] Found seqtk - /usr/local/bin/seqtk [13:04:08] Found parallel - /usr/local/bin/parallel [13:04:08] Found freebayes - /usr/local/bin/freebayes [13:04:08] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [13:04:08] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [13:04:08] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [13:04:08] Found vcfuniq - /usr/local/bin/vcfuniq [13:04:08] Found vcffirstheader - /usr/local/bin/vcffirstheader [13:04:08] Found gzip - /bin/gzip [13:04:08] Found vt - /usr/local/bin/vt [13:04:08] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [13:04:08] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [13:04:08] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [13:04:08] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [13:04:08] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [13:04:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [13:04:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [13:04:08] Please supply a reference FASTA/GBK/EMBL file with --reference
1[13:09:56] This is snippy 4.6.0
Show full stderr[13:09:56] This is snippy 4.6.0 [13:09:56] Written by Torsten Seemann [13:09:56] Obtained from https://github.com/tseemann/snippy [13:09:56] Detected operating system: linux [13:09:56] Enabling bundled linux tools. [13:09:56] Found bwa - /usr/local/bin/bwa [13:09:56] Found bcftools - /usr/local/bin/bcftools [13:09:56] Found samtools - /usr/local/bin/samtools [13:09:56] Found java - /usr/local/bin/java [13:09:56] Found snpEff - /usr/local/bin/snpEff [13:09:56] Found samclip - /usr/local/bin/samclip [13:09:56] Found seqtk - /usr/local/bin/seqtk [13:09:56] Found parallel - /usr/local/bin/parallel [13:09:56] Found freebayes - /usr/local/bin/freebayes [13:09:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [13:09:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [13:09:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [13:09:56] Found vcfuniq - /usr/local/bin/vcfuniq [13:09:56] Found vcffirstheader - /usr/local/bin/vcffirstheader [13:09:56] Found gzip - /bin/gzip [13:09:56] Found vt - /usr/local/bin/vt [13:09:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [13:09:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [13:09:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [13:09:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [13:09:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [13:10:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [13:10:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [13:10:03] Please supply a reference FASTA/GBK/EMBL file with --reference
1[13:10:43] This is snippy 4.6.0
Show full stderr[13:10:43] This is snippy 4.6.0 [13:10:43] Written by Torsten Seemann [13:10:43] Obtained from https://github.com/tseemann/snippy [13:10:43] Detected operating system: linux [13:10:43] Enabling bundled linux tools. [13:10:43] Found bwa - /usr/local/bin/bwa [13:10:43] Found bcftools - /usr/local/bin/bcftools [13:10:43] Found samtools - /usr/local/bin/samtools [13:10:43] Found java - /usr/local/bin/java [13:10:43] Found snpEff - /usr/local/bin/snpEff [13:10:43] Found samclip - /usr/local/bin/samclip [13:10:43] Found seqtk - /usr/local/bin/seqtk [13:10:43] Found parallel - /usr/local/bin/parallel [13:10:43] Found freebayes - /usr/local/bin/freebayes [13:10:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [13:10:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [13:10:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [13:10:43] Found vcfuniq - /usr/local/bin/vcfuniq [13:10:43] Found vcffirstheader - /usr/local/bin/vcffirstheader [13:10:43] Found gzip - /bin/gzip [13:10:43] Found vt - /usr/local/bin/vt [13:10:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [13:10:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [13:10:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [13:10:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [13:10:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [13:10:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [13:10:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [13:10:46] Please supply a reference FASTA/GBK/EMBL file with --reference
1[13:25:39] This is snippy 4.6.0
Show full stderr[13:25:39] This is snippy 4.6.0 [13:25:39] Written by Torsten Seemann [13:25:39] Obtained from https://github.com/tseemann/snippy [13:25:39] Detected operating system: linux [13:25:39] Enabling bundled linux tools. [13:25:39] Found bwa - /usr/local/bin/bwa [13:25:39] Found bcftools - /usr/local/bin/bcftools [13:25:39] Found samtools - /usr/local/bin/samtools [13:25:39] Found java - /usr/local/bin/java [13:25:39] Found snpEff - /usr/local/bin/snpEff [13:25:39] Found samclip - /usr/local/bin/samclip [13:25:39] Found seqtk - /usr/local/bin/seqtk [13:25:39] Found parallel - /usr/local/bin/parallel [13:25:39] Found freebayes - /usr/local/bin/freebayes [13:25:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [13:25:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [13:25:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [13:25:39] Found vcfuniq - /usr/local/bin/vcfuniq [13:25:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [13:25:39] Found gzip - /bin/gzip [13:25:39] Found vt - /usr/local/bin/vt [13:25:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [13:25:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [13:25:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [13:25:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [13:25:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [13:25:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [13:25:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [13:25:41] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:57:49] This is snippy 4.6.0
Show full stderr[12:57:49] This is snippy 4.6.0 [12:57:49] Written by Torsten Seemann [12:57:49] Obtained from https://github.com/tseemann/snippy [12:57:49] Detected operating system: linux [12:57:49] Enabling bundled linux tools. [12:57:49] Found bwa - /usr/local/bin/bwa [12:57:49] Found bcftools - /usr/local/bin/bcftools [12:57:49] Found samtools - /usr/local/bin/samtools [12:57:49] Found java - /usr/local/bin/java [12:57:49] Found snpEff - /usr/local/bin/snpEff [12:57:49] Found samclip - /usr/local/bin/samclip [12:57:49] Found seqtk - /usr/local/bin/seqtk [12:57:49] Found parallel - /usr/local/bin/parallel [12:57:49] Found freebayes - /usr/local/bin/freebayes [12:57:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:57:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:57:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:57:49] Found vcfuniq - /usr/local/bin/vcfuniq [12:57:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:57:49] Found gzip - /bin/gzip [12:57:49] Found vt - /usr/local/bin/vt [12:57:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:57:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:57:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:57:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:57:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:57:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:57:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:57:50] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:58:14] This is snippy 4.6.0
Show full stderr[12:58:14] This is snippy 4.6.0 [12:58:14] Written by Torsten Seemann [12:58:14] Obtained from https://github.com/tseemann/snippy [12:58:14] Detected operating system: linux [12:58:14] Enabling bundled linux tools. [12:58:14] Found bwa - /usr/local/bin/bwa [12:58:14] Found bcftools - /usr/local/bin/bcftools [12:58:14] Found samtools - /usr/local/bin/samtools [12:58:14] Found java - /usr/local/bin/java [12:58:14] Found snpEff - /usr/local/bin/snpEff [12:58:14] Found samclip - /usr/local/bin/samclip [12:58:14] Found seqtk - /usr/local/bin/seqtk [12:58:14] Found parallel - /usr/local/bin/parallel [12:58:14] Found freebayes - /usr/local/bin/freebayes [12:58:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:58:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:58:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:58:14] Found vcfuniq - /usr/local/bin/vcfuniq [12:58:14] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:58:14] Found gzip - /bin/gzip [12:58:14] Found vt - /usr/local/bin/vt [12:58:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:58:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:58:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:58:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:58:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:58:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:58:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:58:15] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:53:29] This is snippy 4.6.0
Show full stderr[12:53:29] This is snippy 4.6.0 [12:53:29] Written by Torsten Seemann [12:53:29] Obtained from https://github.com/tseemann/snippy [12:53:29] Detected operating system: linux [12:53:29] Enabling bundled linux tools. [12:53:29] Found bwa - /usr/local/bin/bwa [12:53:29] Found bcftools - /usr/local/bin/bcftools [12:53:29] Found samtools - /usr/local/bin/samtools [12:53:29] Found java - /usr/local/bin/java [12:53:29] Found snpEff - /usr/local/bin/snpEff [12:53:29] Found samclip - /usr/local/bin/samclip [12:53:29] Found seqtk - /usr/local/bin/seqtk [12:53:29] Found parallel - /usr/local/bin/parallel [12:53:29] Found freebayes - /usr/local/bin/freebayes [12:53:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:53:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:53:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:53:29] Found vcfuniq - /usr/local/bin/vcfuniq [12:53:29] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:53:29] Found gzip - /bin/gzip [12:53:29] Found vt - /usr/local/bin/vt [12:53:29] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:53:29] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:53:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:53:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:53:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:53:30] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:53:30] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:53:30] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:54:11] This is snippy 4.6.0
Show full stderr[12:54:11] This is snippy 4.6.0 [12:54:11] Written by Torsten Seemann [12:54:11] Obtained from https://github.com/tseemann/snippy [12:54:11] Detected operating system: linux [12:54:11] Enabling bundled linux tools. [12:54:11] Found bwa - /usr/local/bin/bwa [12:54:11] Found bcftools - /usr/local/bin/bcftools [12:54:11] Found samtools - /usr/local/bin/samtools [12:54:11] Found java - /usr/local/bin/java [12:54:11] Found snpEff - /usr/local/bin/snpEff [12:54:11] Found samclip - /usr/local/bin/samclip [12:54:11] Found seqtk - /usr/local/bin/seqtk [12:54:11] Found parallel - /usr/local/bin/parallel [12:54:11] Found freebayes - /usr/local/bin/freebayes [12:54:11] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:54:11] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:54:11] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:54:11] Found vcfuniq - /usr/local/bin/vcfuniq [12:54:11] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:54:11] Found gzip - /bin/gzip [12:54:11] Found vt - /usr/local/bin/vt [12:54:11] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:54:11] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:54:11] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:54:11] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:54:11] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:54:12] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:54:12] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:54:12] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:52:48] This is snippy 4.6.0
Show full stderr[12:52:48] This is snippy 4.6.0 [12:52:48] Written by Torsten Seemann [12:52:48] Obtained from https://github.com/tseemann/snippy [12:52:48] Detected operating system: linux [12:52:48] Enabling bundled linux tools. [12:52:48] Found bwa - /usr/local/bin/bwa [12:52:48] Found bcftools - /usr/local/bin/bcftools [12:52:48] Found samtools - /usr/local/bin/samtools [12:52:48] Found java - /usr/local/bin/java [12:52:48] Found snpEff - /usr/local/bin/snpEff [12:52:48] Found samclip - /usr/local/bin/samclip [12:52:48] Found seqtk - /usr/local/bin/seqtk [12:52:48] Found parallel - /usr/local/bin/parallel [12:52:48] Found freebayes - /usr/local/bin/freebayes [12:52:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:52:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:52:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:52:48] Found vcfuniq - /usr/local/bin/vcfuniq [12:52:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:52:48] Found gzip - /bin/gzip [12:52:48] Found vt - /usr/local/bin/vt [12:52:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:52:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:52:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:52:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:52:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:52:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:52:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:52:49] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:58:50] This is snippy 4.6.0
Show full stderr[12:58:50] This is snippy 4.6.0 [12:58:50] Written by Torsten Seemann [12:58:50] Obtained from https://github.com/tseemann/snippy [12:58:50] Detected operating system: linux [12:58:50] Enabling bundled linux tools. [12:58:50] Found bwa - /usr/local/bin/bwa [12:58:50] Found bcftools - /usr/local/bin/bcftools [12:58:50] Found samtools - /usr/local/bin/samtools [12:58:50] Found java - /usr/local/bin/java [12:58:50] Found snpEff - /usr/local/bin/snpEff [12:58:50] Found samclip - /usr/local/bin/samclip [12:58:50] Found seqtk - /usr/local/bin/seqtk [12:58:50] Found parallel - /usr/local/bin/parallel [12:58:50] Found freebayes - /usr/local/bin/freebayes [12:58:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:58:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:58:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:58:50] Found vcfuniq - /usr/local/bin/vcfuniq [12:58:50] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:58:50] Found gzip - /bin/gzip [12:58:50] Found vt - /usr/local/bin/vt [12:58:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:58:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:58:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:58:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:58:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:58:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:58:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:58:51] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:58:53] This is snippy 4.6.0
Show full stderr[12:58:53] This is snippy 4.6.0 [12:58:53] Written by Torsten Seemann [12:58:53] Obtained from https://github.com/tseemann/snippy [12:58:53] Detected operating system: linux [12:58:53] Enabling bundled linux tools. [12:58:53] Found bwa - /usr/local/bin/bwa [12:58:53] Found bcftools - /usr/local/bin/bcftools [12:58:53] Found samtools - /usr/local/bin/samtools [12:58:53] Found java - /usr/local/bin/java [12:58:53] Found snpEff - /usr/local/bin/snpEff [12:58:53] Found samclip - /usr/local/bin/samclip [12:58:53] Found seqtk - /usr/local/bin/seqtk [12:58:53] Found parallel - /usr/local/bin/parallel [12:58:53] Found freebayes - /usr/local/bin/freebayes [12:58:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:58:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:58:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:58:53] Found vcfuniq - /usr/local/bin/vcfuniq [12:58:53] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:58:53] Found gzip - /bin/gzip [12:58:53] Found vt - /usr/local/bin/vt [12:58:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:58:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:58:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:58:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:58:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:58:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:58:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:58:54] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:58:59] This is snippy 4.6.0
Show full stderr[12:58:59] This is snippy 4.6.0 [12:58:59] Written by Torsten Seemann [12:58:59] Obtained from https://github.com/tseemann/snippy [12:58:59] Detected operating system: linux [12:58:59] Enabling bundled linux tools. [12:58:59] Found bwa - /usr/local/bin/bwa [12:58:59] Found bcftools - /usr/local/bin/bcftools [12:58:59] Found samtools - /usr/local/bin/samtools [12:58:59] Found java - /usr/local/bin/java [12:58:59] Found snpEff - /usr/local/bin/snpEff [12:58:59] Found samclip - /usr/local/bin/samclip [12:58:59] Found seqtk - /usr/local/bin/seqtk [12:58:59] Found parallel - /usr/local/bin/parallel [12:58:59] Found freebayes - /usr/local/bin/freebayes [12:58:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:58:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:58:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:58:59] Found vcfuniq - /usr/local/bin/vcfuniq [12:58:59] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:58:59] Found gzip - /bin/gzip [12:58:59] Found vt - /usr/local/bin/vt [12:58:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:58:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:58:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:58:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:58:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:59:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:59:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:59:00] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:59:07] This is snippy 4.6.0
Show full stderr[12:59:07] This is snippy 4.6.0 [12:59:07] Written by Torsten Seemann [12:59:07] Obtained from https://github.com/tseemann/snippy [12:59:07] Detected operating system: linux [12:59:07] Enabling bundled linux tools. [12:59:07] Found bwa - /usr/local/bin/bwa [12:59:07] Found bcftools - /usr/local/bin/bcftools [12:59:07] Found samtools - /usr/local/bin/samtools [12:59:07] Found java - /usr/local/bin/java [12:59:07] Found snpEff - /usr/local/bin/snpEff [12:59:07] Found samclip - /usr/local/bin/samclip [12:59:07] Found seqtk - /usr/local/bin/seqtk [12:59:07] Found parallel - /usr/local/bin/parallel [12:59:07] Found freebayes - /usr/local/bin/freebayes [12:59:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:59:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:59:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:59:07] Found vcfuniq - /usr/local/bin/vcfuniq [12:59:07] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:59:07] Found gzip - /bin/gzip [12:59:07] Found vt - /usr/local/bin/vt [12:59:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:59:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:59:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:59:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:59:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:59:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:59:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:59:08] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:53:44] This is snippy 4.6.0
Show full stderr[12:53:44] This is snippy 4.6.0 [12:53:44] Written by Torsten Seemann [12:53:44] Obtained from https://github.com/tseemann/snippy [12:53:44] Detected operating system: linux [12:53:44] Enabling bundled linux tools. [12:53:44] Found bwa - /usr/local/bin/bwa [12:53:44] Found bcftools - /usr/local/bin/bcftools [12:53:44] Found samtools - /usr/local/bin/samtools [12:53:44] Found java - /usr/local/bin/java [12:53:44] Found snpEff - /usr/local/bin/snpEff [12:53:44] Found samclip - /usr/local/bin/samclip [12:53:44] Found seqtk - /usr/local/bin/seqtk [12:53:44] Found parallel - /usr/local/bin/parallel [12:53:44] Found freebayes - /usr/local/bin/freebayes [12:53:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:53:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:53:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:53:44] Found vcfuniq - /usr/local/bin/vcfuniq [12:53:44] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:53:44] Found gzip - /bin/gzip [12:53:44] Found vt - /usr/local/bin/vt [12:53:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:53:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:53:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:53:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:53:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:53:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:53:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:53:45] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:53:54] This is snippy 4.6.0
Show full stderr[12:53:54] This is snippy 4.6.0 [12:53:54] Written by Torsten Seemann [12:53:54] Obtained from https://github.com/tseemann/snippy [12:53:54] Detected operating system: linux [12:53:54] Enabling bundled linux tools. [12:53:54] Found bwa - /usr/local/bin/bwa [12:53:54] Found bcftools - /usr/local/bin/bcftools [12:53:54] Found samtools - /usr/local/bin/samtools [12:53:54] Found java - /usr/local/bin/java [12:53:54] Found snpEff - /usr/local/bin/snpEff [12:53:54] Found samclip - /usr/local/bin/samclip [12:53:54] Found seqtk - /usr/local/bin/seqtk [12:53:54] Found parallel - /usr/local/bin/parallel [12:53:54] Found freebayes - /usr/local/bin/freebayes [12:53:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:53:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:53:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:53:54] Found vcfuniq - /usr/local/bin/vcfuniq [12:53:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:53:54] Found gzip - /bin/gzip [12:53:54] Found vt - /usr/local/bin/vt [12:53:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:53:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:53:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:53:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:53:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:53:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:53:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:53:55] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:53:57] This is snippy 4.6.0
Show full stderr[12:53:57] This is snippy 4.6.0 [12:53:57] Written by Torsten Seemann [12:53:57] Obtained from https://github.com/tseemann/snippy [12:53:57] Detected operating system: linux [12:53:57] Enabling bundled linux tools. [12:53:57] Found bwa - /usr/local/bin/bwa [12:53:57] Found bcftools - /usr/local/bin/bcftools [12:53:57] Found samtools - /usr/local/bin/samtools [12:53:57] Found java - /usr/local/bin/java [12:53:57] Found snpEff - /usr/local/bin/snpEff [12:53:57] Found samclip - /usr/local/bin/samclip [12:53:57] Found seqtk - /usr/local/bin/seqtk [12:53:57] Found parallel - /usr/local/bin/parallel [12:53:57] Found freebayes - /usr/local/bin/freebayes [12:53:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:53:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:53:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:53:57] Found vcfuniq - /usr/local/bin/vcfuniq [12:53:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:53:58] Found gzip - /bin/gzip [12:53:58] Found vt - /usr/local/bin/vt [12:53:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:53:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:53:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:53:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:53:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:53:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:53:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:53:58] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:59:32] This is snippy 4.6.0
Show full stderr[12:59:32] This is snippy 4.6.0 [12:59:32] Written by Torsten Seemann [12:59:32] Obtained from https://github.com/tseemann/snippy [12:59:32] Detected operating system: linux [12:59:32] Enabling bundled linux tools. [12:59:32] Found bwa - /usr/local/bin/bwa [12:59:32] Found bcftools - /usr/local/bin/bcftools [12:59:32] Found samtools - /usr/local/bin/samtools [12:59:32] Found java - /usr/local/bin/java [12:59:32] Found snpEff - /usr/local/bin/snpEff [12:59:32] Found samclip - /usr/local/bin/samclip [12:59:32] Found seqtk - /usr/local/bin/seqtk [12:59:32] Found parallel - /usr/local/bin/parallel [12:59:32] Found freebayes - /usr/local/bin/freebayes [12:59:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:59:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:59:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:59:32] Found vcfuniq - /usr/local/bin/vcfuniq [12:59:32] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:59:32] Found gzip - /bin/gzip [12:59:32] Found vt - /usr/local/bin/vt [12:59:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:59:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:59:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:59:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:59:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:59:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:59:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:59:33] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:59:46] This is snippy 4.6.0
Show full stderr[12:59:46] This is snippy 4.6.0 [12:59:46] Written by Torsten Seemann [12:59:46] Obtained from https://github.com/tseemann/snippy [12:59:46] Detected operating system: linux [12:59:46] Enabling bundled linux tools. [12:59:46] Found bwa - /usr/local/bin/bwa [12:59:46] Found bcftools - /usr/local/bin/bcftools [12:59:46] Found samtools - /usr/local/bin/samtools [12:59:46] Found java - /usr/local/bin/java [12:59:46] Found snpEff - /usr/local/bin/snpEff [12:59:46] Found samclip - /usr/local/bin/samclip [12:59:46] Found seqtk - /usr/local/bin/seqtk [12:59:46] Found parallel - /usr/local/bin/parallel [12:59:46] Found freebayes - /usr/local/bin/freebayes [12:59:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:59:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:59:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:59:46] Found vcfuniq - /usr/local/bin/vcfuniq [12:59:46] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:59:46] Found gzip - /bin/gzip [12:59:46] Found vt - /usr/local/bin/vt [12:59:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:59:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:59:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:59:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:59:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:59:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:59:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:59:47] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:55:05] This is snippy 4.6.0
Show full stderr[12:55:05] This is snippy 4.6.0 [12:55:05] Written by Torsten Seemann [12:55:05] Obtained from https://github.com/tseemann/snippy [12:55:05] Detected operating system: linux [12:55:05] Enabling bundled linux tools. [12:55:05] Found bwa - /usr/local/bin/bwa [12:55:06] Found bcftools - /usr/local/bin/bcftools [12:55:06] Found samtools - /usr/local/bin/samtools [12:55:06] Found java - /usr/local/bin/java [12:55:06] Found snpEff - /usr/local/bin/snpEff [12:55:06] Found samclip - /usr/local/bin/samclip [12:55:06] Found seqtk - /usr/local/bin/seqtk [12:55:06] Found parallel - /usr/local/bin/parallel [12:55:06] Found freebayes - /usr/local/bin/freebayes [12:55:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:55:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:55:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:55:06] Found vcfuniq - /usr/local/bin/vcfuniq [12:55:06] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:55:06] Found gzip - /bin/gzip [12:55:06] Found vt - /usr/local/bin/vt [12:55:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:55:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:55:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:55:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:55:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:55:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:55:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:55:06] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:55:22] This is snippy 4.6.0
Show full stderr[12:55:22] This is snippy 4.6.0 [12:55:22] Written by Torsten Seemann [12:55:22] Obtained from https://github.com/tseemann/snippy [12:55:22] Detected operating system: linux [12:55:22] Enabling bundled linux tools. [12:55:22] Found bwa - /usr/local/bin/bwa [12:55:22] Found bcftools - /usr/local/bin/bcftools [12:55:23] Found samtools - /usr/local/bin/samtools [12:55:23] Found java - /usr/local/bin/java [12:55:23] Found snpEff - /usr/local/bin/snpEff [12:55:23] Found samclip - /usr/local/bin/samclip [12:55:23] Found seqtk - /usr/local/bin/seqtk [12:55:23] Found parallel - /usr/local/bin/parallel [12:55:23] Found freebayes - /usr/local/bin/freebayes [12:55:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:55:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:55:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:55:23] Found vcfuniq - /usr/local/bin/vcfuniq [12:55:23] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:55:23] Found gzip - /bin/gzip [12:55:23] Found vt - /usr/local/bin/vt [12:55:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:55:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:55:23] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:55:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:55:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:55:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:55:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:55:23] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:55:33] This is snippy 4.6.0
Show full stderr[12:55:33] This is snippy 4.6.0 [12:55:33] Written by Torsten Seemann [12:55:33] Obtained from https://github.com/tseemann/snippy [12:55:33] Detected operating system: linux [12:55:33] Enabling bundled linux tools. [12:55:33] Found bwa - /usr/local/bin/bwa [12:55:33] Found bcftools - /usr/local/bin/bcftools [12:55:33] Found samtools - /usr/local/bin/samtools [12:55:33] Found java - /usr/local/bin/java [12:55:33] Found snpEff - /usr/local/bin/snpEff [12:55:33] Found samclip - /usr/local/bin/samclip [12:55:33] Found seqtk - /usr/local/bin/seqtk [12:55:33] Found parallel - /usr/local/bin/parallel [12:55:33] Found freebayes - /usr/local/bin/freebayes [12:55:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:55:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:55:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:55:33] Found vcfuniq - /usr/local/bin/vcfuniq [12:55:33] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:55:33] Found gzip - /bin/gzip [12:55:33] Found vt - /usr/local/bin/vt [12:55:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:55:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:55:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:55:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:55:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:55:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:55:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:55:33] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:55:32] This is snippy 4.6.0
Show full stderr[12:55:32] This is snippy 4.6.0 [12:55:32] Written by Torsten Seemann [12:55:32] Obtained from https://github.com/tseemann/snippy [12:55:32] Detected operating system: linux [12:55:32] Enabling bundled linux tools. [12:55:32] Found bwa - /usr/local/bin/bwa [12:55:32] Found bcftools - /usr/local/bin/bcftools [12:55:32] Found samtools - /usr/local/bin/samtools [12:55:32] Found java - /usr/local/bin/java [12:55:32] Found snpEff - /usr/local/bin/snpEff [12:55:32] Found samclip - /usr/local/bin/samclip [12:55:32] Found seqtk - /usr/local/bin/seqtk [12:55:32] Found parallel - /usr/local/bin/parallel [12:55:32] Found freebayes - /usr/local/bin/freebayes [12:55:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:55:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:55:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:55:33] Found vcfuniq - /usr/local/bin/vcfuniq [12:55:33] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:55:33] Found gzip - /bin/gzip [12:55:33] Found vt - /usr/local/bin/vt [12:55:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:55:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:55:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:55:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:55:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:55:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:55:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:55:33] Please supply a reference FASTA/GBK/EMBL file with --reference
1[13:00:17] This is snippy 4.6.0
Show full stderr[13:00:17] This is snippy 4.6.0 [13:00:17] Written by Torsten Seemann [13:00:17] Obtained from https://github.com/tseemann/snippy [13:00:17] Detected operating system: linux [13:00:17] Enabling bundled linux tools. [13:00:17] Found bwa - /usr/local/bin/bwa [13:00:17] Found bcftools - /usr/local/bin/bcftools [13:00:17] Found samtools - /usr/local/bin/samtools [13:00:17] Found java - /usr/local/bin/java [13:00:17] Found snpEff - /usr/local/bin/snpEff [13:00:17] Found samclip - /usr/local/bin/samclip [13:00:17] Found seqtk - /usr/local/bin/seqtk [13:00:17] Found parallel - /usr/local/bin/parallel [13:00:17] Found freebayes - /usr/local/bin/freebayes [13:00:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [13:00:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [13:00:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [13:00:17] Found vcfuniq - /usr/local/bin/vcfuniq [13:00:17] Found vcffirstheader - /usr/local/bin/vcffirstheader [13:00:17] Found gzip - /bin/gzip [13:00:17] Found vt - /usr/local/bin/vt [13:00:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [13:00:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [13:00:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [13:00:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [13:00:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [13:00:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [13:00:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [13:00:18] Please supply a reference FASTA/GBK/EMBL file with --reference
1[19:40:20] This is snippy 4.6.0
Show full stderr[19:40:20] This is snippy 4.6.0 [19:40:20] Written by Torsten Seemann [19:40:20] Obtained from https://github.com/tseemann/snippy [19:40:20] Detected operating system: linux [19:40:20] Enabling bundled linux tools. [19:40:20] Found bwa - /usr/local/bin/bwa [19:40:20] Found bcftools - /usr/local/bin/bcftools [19:40:20] Found samtools - /usr/local/bin/samtools [19:40:20] Found java - /usr/local/bin/java [19:40:20] Found snpEff - /usr/local/bin/snpEff [19:40:20] Found samclip - /usr/local/bin/samclip [19:40:20] Found seqtk - /usr/local/bin/seqtk [19:40:20] Found parallel - /usr/local/bin/parallel [19:40:20] Found freebayes - /usr/local/bin/freebayes [19:40:20] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [19:40:20] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [19:40:20] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [19:40:20] Found vcfuniq - /usr/local/bin/vcfuniq [19:40:20] Found vcffirstheader - /usr/local/bin/vcffirstheader [19:40:20] Found gzip - /bin/gzip [19:40:20] Found vt - /usr/local/bin/vt [19:40:20] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [19:40:20] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [19:40:20] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [19:40:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [19:40:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [19:40:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [19:40:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [19:40:20] Please supply a reference FASTA/GBK/EMBL file with --reference
1[19:40:52] This is snippy 4.6.0
Show full stderr[19:40:52] This is snippy 4.6.0 [19:40:52] Written by Torsten Seemann [19:40:52] Obtained from https://github.com/tseemann/snippy [19:40:52] Detected operating system: linux [19:40:52] Enabling bundled linux tools. [19:40:52] Found bwa - /usr/local/bin/bwa [19:40:52] Found bcftools - /usr/local/bin/bcftools [19:40:52] Found samtools - /usr/local/bin/samtools [19:40:52] Found java - /usr/local/bin/java [19:40:52] Found snpEff - /usr/local/bin/snpEff [19:40:52] Found samclip - /usr/local/bin/samclip [19:40:52] Found seqtk - /usr/local/bin/seqtk [19:40:52] Found parallel - /usr/local/bin/parallel [19:40:52] Found freebayes - /usr/local/bin/freebayes [19:40:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [19:40:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [19:40:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [19:40:52] Found vcfuniq - /usr/local/bin/vcfuniq [19:40:52] Found vcffirstheader - /usr/local/bin/vcffirstheader [19:40:52] Found gzip - /bin/gzip [19:40:52] Found vt - /usr/local/bin/vt [19:40:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [19:40:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [19:40:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [19:40:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [19:40:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [19:40:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [19:40:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [19:40:53] Please supply a reference FASTA/GBK/EMBL file with --reference
1[19:46:59] This is snippy 4.6.0
Show full stderr[19:46:59] This is snippy 4.6.0 [19:46:59] Written by Torsten Seemann [19:46:59] Obtained from https://github.com/tseemann/snippy [19:46:59] Detected operating system: linux [19:46:59] Enabling bundled linux tools. [19:46:59] Found bwa - /usr/local/bin/bwa [19:46:59] Found bcftools - /usr/local/bin/bcftools [19:46:59] Found samtools - /usr/local/bin/samtools [19:46:59] Found java - /usr/local/bin/java [19:46:59] Found snpEff - /usr/local/bin/snpEff [19:46:59] Found samclip - /usr/local/bin/samclip [19:46:59] Found seqtk - /usr/local/bin/seqtk [19:46:59] Found parallel - /usr/local/bin/parallel [19:46:59] Found freebayes - /usr/local/bin/freebayes [19:46:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [19:46:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [19:46:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [19:46:59] Found vcfuniq - /usr/local/bin/vcfuniq [19:46:59] Found vcffirstheader - /usr/local/bin/vcffirstheader [19:46:59] Found gzip - /bin/gzip [19:46:59] Found vt - /usr/local/bin/vt [19:46:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [19:46:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [19:47:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [19:47:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [19:47:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [19:47:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [19:47:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [19:47:03] Please supply a reference FASTA/GBK/EMBL file with --reference
1[19:47:00] This is snippy 4.6.0
Show full stderr[19:47:00] This is snippy 4.6.0 [19:47:00] Written by Torsten Seemann [19:47:00] Obtained from https://github.com/tseemann/snippy [19:47:00] Detected operating system: linux [19:47:00] Enabling bundled linux tools. [19:47:00] Found bwa - /usr/local/bin/bwa [19:47:00] Found bcftools - /usr/local/bin/bcftools [19:47:00] Found samtools - /usr/local/bin/samtools [19:47:00] Found java - /usr/local/bin/java [19:47:00] Found snpEff - /usr/local/bin/snpEff [19:47:00] Found samclip - /usr/local/bin/samclip [19:47:00] Found seqtk - /usr/local/bin/seqtk [19:47:00] Found parallel - /usr/local/bin/parallel [19:47:00] Found freebayes - /usr/local/bin/freebayes [19:47:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [19:47:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [19:47:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [19:47:00] Found vcfuniq - /usr/local/bin/vcfuniq [19:47:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [19:47:00] Found gzip - /bin/gzip [19:47:00] Found vt - /usr/local/bin/vt [19:47:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [19:47:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [19:47:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [19:47:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [19:47:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [19:47:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [19:47:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [19:47:00] Please supply a reference FASTA/GBK/EMBL file with --reference
1[19:40:58] This is snippy 4.6.0
Show full stderr[19:40:58] This is snippy 4.6.0 [19:40:58] Written by Torsten Seemann [19:40:58] Obtained from https://github.com/tseemann/snippy [19:40:58] Detected operating system: linux [19:40:58] Enabling bundled linux tools. [19:40:58] Found bwa - /usr/local/bin/bwa [19:40:58] Found bcftools - /usr/local/bin/bcftools [19:40:58] Found samtools - /usr/local/bin/samtools [19:40:58] Found java - /usr/local/bin/java [19:40:58] Found snpEff - /usr/local/bin/snpEff [19:40:58] Found samclip - /usr/local/bin/samclip [19:40:58] Found seqtk - /usr/local/bin/seqtk [19:40:58] Found parallel - /usr/local/bin/parallel [19:40:58] Found freebayes - /usr/local/bin/freebayes [19:40:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [19:40:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [19:40:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [19:40:58] Found vcfuniq - /usr/local/bin/vcfuniq [19:40:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [19:40:58] Found gzip - /bin/gzip [19:40:58] Found vt - /usr/local/bin/vt [19:40:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [19:40:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [19:40:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [19:40:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [19:40:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [19:40:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [19:40:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [19:40:59] Please supply a reference FASTA/GBK/EMBL file with --reference
1[19:41:08] This is snippy 4.6.0
Show full stderr[19:41:08] This is snippy 4.6.0 [19:41:08] Written by Torsten Seemann [19:41:08] Obtained from https://github.com/tseemann/snippy [19:41:08] Detected operating system: linux [19:41:08] Enabling bundled linux tools. [19:41:08] Found bwa - /usr/local/bin/bwa [19:41:08] Found bcftools - /usr/local/bin/bcftools [19:41:08] Found samtools - /usr/local/bin/samtools [19:41:08] Found java - /usr/local/bin/java [19:41:08] Found snpEff - /usr/local/bin/snpEff [19:41:08] Found samclip - /usr/local/bin/samclip [19:41:08] Found seqtk - /usr/local/bin/seqtk [19:41:08] Found parallel - /usr/local/bin/parallel [19:41:08] Found freebayes - /usr/local/bin/freebayes [19:41:08] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [19:41:08] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [19:41:08] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [19:41:08] Found vcfuniq - /usr/local/bin/vcfuniq [19:41:08] Found vcffirstheader - /usr/local/bin/vcffirstheader [19:41:08] Found gzip - /bin/gzip [19:41:08] Found vt - /usr/local/bin/vt [19:41:08] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [19:41:08] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [19:41:08] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [19:41:08] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [19:41:08] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [19:41:09] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [19:41:09] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [19:41:09] Please supply a reference FASTA/GBK/EMBL file with --reference
1[19:52:24] This is snippy 4.6.0
Show full stderr[19:52:24] This is snippy 4.6.0 [19:52:24] Written by Torsten Seemann [19:52:24] Obtained from https://github.com/tseemann/snippy [19:52:24] Detected operating system: linux [19:52:24] Enabling bundled linux tools. [19:52:24] Found bwa - /usr/local/bin/bwa [19:52:24] Found bcftools - /usr/local/bin/bcftools [19:52:24] Found samtools - /usr/local/bin/samtools [19:52:24] Found java - /usr/local/bin/java [19:52:24] Found snpEff - /usr/local/bin/snpEff [19:52:24] Found samclip - /usr/local/bin/samclip [19:52:24] Found seqtk - /usr/local/bin/seqtk [19:52:24] Found parallel - /usr/local/bin/parallel [19:52:24] Found freebayes - /usr/local/bin/freebayes [19:52:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [19:52:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [19:52:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [19:52:24] Found vcfuniq - /usr/local/bin/vcfuniq [19:52:24] Found vcffirstheader - /usr/local/bin/vcffirstheader [19:52:24] Found gzip - /bin/gzip [19:52:24] Found vt - /usr/local/bin/vt [19:52:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [19:52:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [19:52:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [19:52:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [19:52:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [19:52:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [19:52:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [19:52:25] Please supply a reference FASTA/GBK/EMBL file with --reference
1[19:40:23] This is snippy 4.6.0
Show full stderr[19:40:23] This is snippy 4.6.0 [19:40:23] Written by Torsten Seemann [19:40:23] Obtained from https://github.com/tseemann/snippy [19:40:23] Detected operating system: linux [19:40:23] Enabling bundled linux tools. [19:40:23] Found bwa - /usr/local/bin/bwa [19:40:23] Found bcftools - /usr/local/bin/bcftools [19:40:23] Found samtools - /usr/local/bin/samtools [19:40:23] Found java - /usr/local/bin/java [19:40:23] Found snpEff - /usr/local/bin/snpEff [19:40:23] Found samclip - /usr/local/bin/samclip [19:40:23] Found seqtk - /usr/local/bin/seqtk [19:40:23] Found parallel - /usr/local/bin/parallel [19:40:23] Found freebayes - /usr/local/bin/freebayes [19:40:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [19:40:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [19:40:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [19:40:23] Found vcfuniq - /usr/local/bin/vcfuniq [19:40:23] Found vcffirstheader - /usr/local/bin/vcffirstheader [19:40:23] Found gzip - /bin/gzip [19:40:23] Found vt - /usr/local/bin/vt [19:40:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [19:40:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [19:40:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [19:40:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [19:40:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [19:40:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [19:40:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [19:40:24] Please supply a reference FASTA/GBK/EMBL file with --reference
1[19:46:27] This is snippy 4.6.0
Show full stderr[19:46:27] This is snippy 4.6.0 [19:46:27] Written by Torsten Seemann [19:46:27] Obtained from https://github.com/tseemann/snippy [19:46:27] Detected operating system: linux [19:46:27] Enabling bundled linux tools. [19:46:27] Found bwa - /usr/local/bin/bwa [19:46:27] Found bcftools - /usr/local/bin/bcftools [19:46:27] Found samtools - /usr/local/bin/samtools [19:46:27] Found java - /usr/local/bin/java [19:46:27] Found snpEff - /usr/local/bin/snpEff [19:46:27] Found samclip - /usr/local/bin/samclip [19:46:27] Found seqtk - /usr/local/bin/seqtk [19:46:27] Found parallel - /usr/local/bin/parallel [19:46:27] Found freebayes - /usr/local/bin/freebayes [19:46:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [19:46:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [19:46:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [19:46:27] Found vcfuniq - /usr/local/bin/vcfuniq [19:46:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [19:46:27] Found gzip - /bin/gzip [19:46:27] Found vt - /usr/local/bin/vt [19:46:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [19:46:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [19:46:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [19:46:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [19:46:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [19:46:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [19:46:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [19:46:28] Please supply a reference FASTA/GBK/EMBL file with --reference
1[19:40:42] This is snippy 4.6.0
Show full stderr[19:40:42] This is snippy 4.6.0 [19:40:42] Written by Torsten Seemann [19:40:42] Obtained from https://github.com/tseemann/snippy [19:40:42] Detected operating system: linux [19:40:42] Enabling bundled linux tools. [19:40:42] Found bwa - /usr/local/bin/bwa [19:40:42] Found bcftools - /usr/local/bin/bcftools [19:40:42] Found samtools - /usr/local/bin/samtools [19:40:42] Found java - /usr/local/bin/java [19:40:42] Found snpEff - /usr/local/bin/snpEff [19:40:42] Found samclip - /usr/local/bin/samclip [19:40:42] Found seqtk - /usr/local/bin/seqtk [19:40:42] Found parallel - /usr/local/bin/parallel [19:40:42] Found freebayes - /usr/local/bin/freebayes [19:40:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [19:40:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [19:40:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [19:40:42] Found vcfuniq - /usr/local/bin/vcfuniq [19:40:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [19:40:42] Found gzip - /bin/gzip [19:40:42] Found vt - /usr/local/bin/vt [19:40:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [19:40:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [19:40:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [19:40:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [19:40:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [19:40:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [19:40:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [19:40:43] Please supply a reference FASTA/GBK/EMBL file with --reference
1[19:46:24] This is snippy 4.6.0
Show full stderr[19:46:24] This is snippy 4.6.0 [19:46:24] Written by Torsten Seemann [19:46:24] Obtained from https://github.com/tseemann/snippy [19:46:24] Detected operating system: linux [19:46:24] Enabling bundled linux tools. [19:46:24] Found bwa - /usr/local/bin/bwa [19:46:24] Found bcftools - /usr/local/bin/bcftools [19:46:24] Found samtools - /usr/local/bin/samtools [19:46:24] Found java - /usr/local/bin/java [19:46:24] Found snpEff - /usr/local/bin/snpEff [19:46:24] Found samclip - /usr/local/bin/samclip [19:46:24] Found seqtk - /usr/local/bin/seqtk [19:46:24] Found parallel - /usr/local/bin/parallel [19:46:24] Found freebayes - /usr/local/bin/freebayes [19:46:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [19:46:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [19:46:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [19:46:24] Found vcfuniq - /usr/local/bin/vcfuniq [19:46:24] Found vcffirstheader - /usr/local/bin/vcffirstheader [19:46:24] Found gzip - /bin/gzip [19:46:24] Found vt - /usr/local/bin/vt [19:46:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [19:46:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [19:46:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [19:46:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [19:46:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [19:46:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [19:46:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [19:46:28] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:55:33] This is snippy 4.6.0
Show full stderr[06:55:33] This is snippy 4.6.0 [06:55:33] Written by Torsten Seemann [06:55:33] Obtained from https://github.com/tseemann/snippy [06:55:33] Detected operating system: linux [06:55:33] Enabling bundled linux tools. [06:55:33] Found bwa - /usr/local/bin/bwa [06:55:33] Found bcftools - /usr/local/bin/bcftools [06:55:33] Found samtools - /usr/local/bin/samtools [06:55:33] Found java - /usr/local/bin/java [06:55:33] Found snpEff - /usr/local/bin/snpEff [06:55:33] Found samclip - /usr/local/bin/samclip [06:55:33] Found seqtk - /usr/local/bin/seqtk [06:55:33] Found parallel - /usr/local/bin/parallel [06:55:33] Found freebayes - /usr/local/bin/freebayes [06:55:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:55:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:55:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:55:33] Found vcfuniq - /usr/local/bin/vcfuniq [06:55:33] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:55:33] Found gzip - /bin/gzip [06:55:33] Found vt - /usr/local/bin/vt [06:55:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:55:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:55:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:55:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:55:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:55:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:55:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:55:34] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:06:51] This is snippy 4.6.0
Show full stderr[07:06:51] This is snippy 4.6.0 [07:06:51] Written by Torsten Seemann [07:06:51] Obtained from https://github.com/tseemann/snippy [07:06:51] Detected operating system: linux [07:06:51] Enabling bundled linux tools. [07:06:51] Found bwa - /usr/local/bin/bwa [07:06:51] Found bcftools - /usr/local/bin/bcftools [07:06:51] Found samtools - /usr/local/bin/samtools [07:06:51] Found java - /usr/local/bin/java [07:06:51] Found snpEff - /usr/local/bin/snpEff [07:06:51] Found samclip - /usr/local/bin/samclip [07:06:51] Found seqtk - /usr/local/bin/seqtk [07:06:51] Found parallel - /usr/local/bin/parallel [07:06:51] Found freebayes - /usr/local/bin/freebayes [07:06:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:06:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:06:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:06:51] Found vcfuniq - /usr/local/bin/vcfuniq [07:06:51] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:06:51] Found gzip - /bin/gzip [07:06:51] Found vt - /usr/local/bin/vt [07:06:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:06:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:06:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:06:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:06:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:06:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:06:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:06:52] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:07:06] This is snippy 4.6.0
Show full stderr[07:07:06] This is snippy 4.6.0 [07:07:06] Written by Torsten Seemann [07:07:06] Obtained from https://github.com/tseemann/snippy [07:07:06] Detected operating system: linux [07:07:06] Enabling bundled linux tools. [07:07:06] Found bwa - /usr/local/bin/bwa [07:07:06] Found bcftools - /usr/local/bin/bcftools [07:07:06] Found samtools - /usr/local/bin/samtools [07:07:06] Found java - /usr/local/bin/java [07:07:06] Found snpEff - /usr/local/bin/snpEff [07:07:06] Found samclip - /usr/local/bin/samclip [07:07:06] Found seqtk - /usr/local/bin/seqtk [07:07:06] Found parallel - /usr/local/bin/parallel [07:07:06] Found freebayes - /usr/local/bin/freebayes [07:07:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:07:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:07:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:07:06] Found vcfuniq - /usr/local/bin/vcfuniq [07:07:06] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:07:06] Found gzip - /bin/gzip [07:07:06] Found vt - /usr/local/bin/vt [07:07:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:07:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:07:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:07:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:07:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:07:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:07:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:07:07] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:24:06] This is snippy 4.6.0
Show full stderr[07:24:06] This is snippy 4.6.0 [07:24:06] Written by Torsten Seemann [07:24:06] Obtained from https://github.com/tseemann/snippy [07:24:06] Detected operating system: linux [07:24:06] Enabling bundled linux tools. [07:24:06] Found bwa - /usr/local/bin/bwa [07:24:06] Found bcftools - /usr/local/bin/bcftools [07:24:06] Found samtools - /usr/local/bin/samtools [07:24:06] Found java - /usr/local/bin/java [07:24:06] Found snpEff - /usr/local/bin/snpEff [07:24:06] Found samclip - /usr/local/bin/samclip [07:24:06] Found seqtk - /usr/local/bin/seqtk [07:24:06] Found parallel - /usr/local/bin/parallel [07:24:06] Found freebayes - /usr/local/bin/freebayes [07:24:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:24:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:24:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:24:06] Found vcfuniq - /usr/local/bin/vcfuniq [07:24:06] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:24:06] Found gzip - /bin/gzip [07:24:06] Found vt - /usr/local/bin/vt [07:24:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:24:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:24:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:24:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:24:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:24:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:24:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:24:07] Please supply a reference FASTA/GBK/EMBL file with --reference
1[08:02:30] This is snippy 4.6.0
Show full stderr[08:02:30] This is snippy 4.6.0 [08:02:30] Written by Torsten Seemann [08:02:30] Obtained from https://github.com/tseemann/snippy [08:02:30] Detected operating system: linux [08:02:30] Enabling bundled linux tools. [08:02:30] Found bwa - /usr/local/bin/bwa [08:02:30] Found bcftools - /usr/local/bin/bcftools [08:02:30] Found samtools - /usr/local/bin/samtools [08:02:30] Found java - /usr/local/bin/java [08:02:30] Found snpEff - /usr/local/bin/snpEff [08:02:30] Found samclip - /usr/local/bin/samclip [08:02:30] Found seqtk - /usr/local/bin/seqtk [08:02:30] Found parallel - /usr/local/bin/parallel [08:02:30] Found freebayes - /usr/local/bin/freebayes [08:02:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:02:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:02:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:02:30] Found vcfuniq - /usr/local/bin/vcfuniq [08:02:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:02:30] Found gzip - /bin/gzip [08:02:30] Found vt - /usr/local/bin/vt [08:02:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:02:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:02:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:02:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:02:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:02:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:02:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:02:31] Please supply a reference FASTA/GBK/EMBL file with --reference
1[08:08:52] This is snippy 4.6.0
Show full stderr[08:08:52] This is snippy 4.6.0 [08:08:52] Written by Torsten Seemann [08:08:52] Obtained from https://github.com/tseemann/snippy [08:08:52] Detected operating system: linux [08:08:52] Enabling bundled linux tools. [08:08:52] Found bwa - /usr/local/bin/bwa [08:08:52] Found bcftools - /usr/local/bin/bcftools [08:08:52] Found samtools - /usr/local/bin/samtools [08:08:52] Found java - /usr/local/bin/java [08:08:52] Found snpEff - /usr/local/bin/snpEff [08:08:52] Found samclip - /usr/local/bin/samclip [08:08:52] Found seqtk - /usr/local/bin/seqtk [08:08:52] Found parallel - /usr/local/bin/parallel [08:08:52] Found freebayes - /usr/local/bin/freebayes [08:08:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:08:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:08:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:08:52] Found vcfuniq - /usr/local/bin/vcfuniq [08:08:52] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:08:52] Found gzip - /bin/gzip [08:08:52] Found vt - /usr/local/bin/vt [08:08:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:08:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:08:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:08:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:08:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:08:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:08:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:08:53] Please supply a reference FASTA/GBK/EMBL file with --reference
1[08:14:54] This is snippy 4.6.0
Show full stderr[08:14:54] This is snippy 4.6.0 [08:14:54] Written by Torsten Seemann [08:14:54] Obtained from https://github.com/tseemann/snippy [08:14:54] Detected operating system: linux [08:14:54] Enabling bundled linux tools. [08:14:54] Found bwa - /usr/local/bin/bwa [08:14:54] Found bcftools - /usr/local/bin/bcftools [08:14:54] Found samtools - /usr/local/bin/samtools [08:14:54] Found java - /usr/local/bin/java [08:14:54] Found snpEff - /usr/local/bin/snpEff [08:14:54] Found samclip - /usr/local/bin/samclip [08:14:54] Found seqtk - /usr/local/bin/seqtk [08:14:54] Found parallel - /usr/local/bin/parallel [08:14:54] Found freebayes - /usr/local/bin/freebayes [08:14:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:14:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:14:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:14:54] Found vcfuniq - /usr/local/bin/vcfuniq [08:14:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:14:54] Found gzip - /bin/gzip [08:14:54] Found vt - /usr/local/bin/vt [08:14:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:14:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:14:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:14:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:14:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:14:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:14:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:14:55] Please supply a reference FASTA/GBK/EMBL file with --reference
1[08:15:52] This is snippy 4.6.0
Show full stderr[08:15:52] This is snippy 4.6.0 [08:15:52] Written by Torsten Seemann [08:15:52] Obtained from https://github.com/tseemann/snippy [08:15:52] Detected operating system: linux [08:15:52] Enabling bundled linux tools. [08:15:52] Found bwa - /usr/local/bin/bwa [08:15:52] Found bcftools - /usr/local/bin/bcftools [08:15:52] Found samtools - /usr/local/bin/samtools [08:15:52] Found java - /usr/local/bin/java [08:15:52] Found snpEff - /usr/local/bin/snpEff [08:15:52] Found samclip - /usr/local/bin/samclip [08:15:52] Found seqtk - /usr/local/bin/seqtk [08:15:52] Found parallel - /usr/local/bin/parallel [08:15:52] Found freebayes - /usr/local/bin/freebayes [08:15:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:15:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:15:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:15:52] Found vcfuniq - /usr/local/bin/vcfuniq [08:15:52] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:15:52] Found gzip - /bin/gzip [08:15:52] Found vt - /usr/local/bin/vt [08:15:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:15:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:15:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:15:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:15:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:15:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:15:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:15:53] Please supply a reference FASTA/GBK/EMBL file with --reference
1[08:42:07] This is snippy 4.6.0
Show full stderr[08:42:07] This is snippy 4.6.0 [08:42:07] Written by Torsten Seemann [08:42:07] Obtained from https://github.com/tseemann/snippy [08:42:07] Detected operating system: linux [08:42:07] Enabling bundled linux tools. [08:42:07] Found bwa - /usr/local/bin/bwa [08:42:07] Found bcftools - /usr/local/bin/bcftools [08:42:07] Found samtools - /usr/local/bin/samtools [08:42:07] Found java - /usr/local/bin/java [08:42:07] Found snpEff - /usr/local/bin/snpEff [08:42:07] Found samclip - /usr/local/bin/samclip [08:42:07] Found seqtk - /usr/local/bin/seqtk [08:42:07] Found parallel - /usr/local/bin/parallel [08:42:07] Found freebayes - /usr/local/bin/freebayes [08:42:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:42:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:42:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:42:07] Found vcfuniq - /usr/local/bin/vcfuniq [08:42:07] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:42:07] Found gzip - /bin/gzip [08:42:07] Found vt - /usr/local/bin/vt [08:42:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:42:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:42:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:42:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:42:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:42:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:42:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:42:08] Please supply a reference FASTA/GBK/EMBL file with --reference
1[08:48:49] This is snippy 4.6.0
Show full stderr[08:48:49] This is snippy 4.6.0 [08:48:49] Written by Torsten Seemann [08:48:49] Obtained from https://github.com/tseemann/snippy [08:48:49] Detected operating system: linux [08:48:49] Enabling bundled linux tools. [08:48:49] Found bwa - /usr/local/bin/bwa [08:48:49] Found bcftools - /usr/local/bin/bcftools [08:48:49] Found samtools - /usr/local/bin/samtools [08:48:49] Found java - /usr/local/bin/java [08:48:49] Found snpEff - /usr/local/bin/snpEff [08:48:49] Found samclip - /usr/local/bin/samclip [08:48:49] Found seqtk - /usr/local/bin/seqtk [08:48:49] Found parallel - /usr/local/bin/parallel [08:48:49] Found freebayes - /usr/local/bin/freebayes [08:48:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:48:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:48:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:48:49] Found vcfuniq - /usr/local/bin/vcfuniq [08:48:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:48:49] Found gzip - /bin/gzip [08:48:49] Found vt - /usr/local/bin/vt [08:48:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:48:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:48:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:48:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:48:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:48:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:48:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:48:49] Please supply a reference FASTA/GBK/EMBL file with --reference
1[08:48:37] This is snippy 4.6.0
Show full stderr[08:48:37] This is snippy 4.6.0 [08:48:37] Written by Torsten Seemann [08:48:37] Obtained from https://github.com/tseemann/snippy [08:48:37] Detected operating system: linux [08:48:37] Enabling bundled linux tools. [08:48:37] Found bwa - /usr/local/bin/bwa [08:48:37] Found bcftools - /usr/local/bin/bcftools [08:48:37] Found samtools - /usr/local/bin/samtools [08:48:37] Found java - /usr/local/bin/java [08:48:37] Found snpEff - /usr/local/bin/snpEff [08:48:37] Found samclip - /usr/local/bin/samclip [08:48:37] Found seqtk - /usr/local/bin/seqtk [08:48:37] Found parallel - /usr/local/bin/parallel [08:48:37] Found freebayes - /usr/local/bin/freebayes [08:48:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:48:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:48:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:48:37] Found vcfuniq - /usr/local/bin/vcfuniq [08:48:37] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:48:37] Found gzip - /bin/gzip [08:48:37] Found vt - /usr/local/bin/vt [08:48:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:48:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:48:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:48:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:48:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:48:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:48:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:48:38] Please supply a reference FASTA/GBK/EMBL file with --reference
1[09:01:59] This is snippy 4.6.0
Show full stderr[09:01:59] This is snippy 4.6.0 [09:01:59] Written by Torsten Seemann [09:01:59] Obtained from https://github.com/tseemann/snippy [09:01:59] Detected operating system: linux [09:01:59] Enabling bundled linux tools. [09:01:59] Found bwa - /usr/local/bin/bwa [09:01:59] Found bcftools - /usr/local/bin/bcftools [09:01:59] Found samtools - /usr/local/bin/samtools [09:01:59] Found java - /usr/local/bin/java [09:01:59] Found snpEff - /usr/local/bin/snpEff [09:01:59] Found samclip - /usr/local/bin/samclip [09:01:59] Found seqtk - /usr/local/bin/seqtk [09:01:59] Found parallel - /usr/local/bin/parallel [09:01:59] Found freebayes - /usr/local/bin/freebayes [09:01:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [09:01:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [09:01:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [09:01:59] Found vcfuniq - /usr/local/bin/vcfuniq [09:01:59] Found vcffirstheader - /usr/local/bin/vcffirstheader [09:01:59] Found gzip - /bin/gzip [09:01:59] Found vt - /usr/local/bin/vt [09:01:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [09:01:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [09:01:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [09:01:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [09:01:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [09:02:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [09:02:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [09:02:00] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:45:21] This is snippy 4.6.0
Show full stderr[14:45:21] This is snippy 4.6.0 [14:45:21] Written by Torsten Seemann [14:45:21] Obtained from https://github.com/tseemann/snippy [14:45:21] Detected operating system: linux [14:45:21] Enabling bundled linux tools. [14:45:21] Found bwa - /usr/local/bin/bwa [14:45:21] Found bcftools - /usr/local/bin/bcftools [14:45:21] Found samtools - /usr/local/bin/samtools [14:45:21] Found java - /usr/local/bin/java [14:45:21] Found snpEff - /usr/local/bin/snpEff [14:45:21] Found samclip - /usr/local/bin/samclip [14:45:21] Found seqtk - /usr/local/bin/seqtk [14:45:21] Found parallel - /usr/local/bin/parallel [14:45:21] Found freebayes - /usr/local/bin/freebayes [14:45:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:45:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:45:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:45:21] Found vcfuniq - /usr/local/bin/vcfuniq [14:45:21] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:45:21] Found gzip - /bin/gzip [14:45:21] Found vt - /usr/local/bin/vt [14:45:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:45:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:45:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:45:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:45:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:45:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:45:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:45:22] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:45:27] This is snippy 4.6.0
Show full stderr[14:45:27] This is snippy 4.6.0 [14:45:27] Written by Torsten Seemann [14:45:27] Obtained from https://github.com/tseemann/snippy [14:45:27] Detected operating system: linux [14:45:27] Enabling bundled linux tools. [14:45:27] Found bwa - /usr/local/bin/bwa [14:45:27] Found bcftools - /usr/local/bin/bcftools [14:45:27] Found samtools - /usr/local/bin/samtools [14:45:27] Found java - /usr/local/bin/java [14:45:27] Found snpEff - /usr/local/bin/snpEff [14:45:27] Found samclip - /usr/local/bin/samclip [14:45:27] Found seqtk - /usr/local/bin/seqtk [14:45:27] Found parallel - /usr/local/bin/parallel [14:45:27] Found freebayes - /usr/local/bin/freebayes [14:45:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:45:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:45:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:45:27] Found vcfuniq - /usr/local/bin/vcfuniq [14:45:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:45:27] Found gzip - /bin/gzip [14:45:27] Found vt - /usr/local/bin/vt [14:45:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:45:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:45:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:45:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:45:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:45:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:45:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:45:28] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:56:57] This is snippy 4.6.0
Show full stderr[14:56:57] This is snippy 4.6.0 [14:56:57] Written by Torsten Seemann [14:56:57] Obtained from https://github.com/tseemann/snippy [14:56:57] Detected operating system: linux [14:56:57] Enabling bundled linux tools. [14:56:57] Found bwa - /usr/local/bin/bwa [14:56:57] Found bcftools - /usr/local/bin/bcftools [14:56:57] Found samtools - /usr/local/bin/samtools [14:56:57] Found java - /usr/local/bin/java [14:56:57] Found snpEff - /usr/local/bin/snpEff [14:56:57] Found samclip - /usr/local/bin/samclip [14:56:57] Found seqtk - /usr/local/bin/seqtk [14:56:57] Found parallel - /usr/local/bin/parallel [14:56:57] Found freebayes - /usr/local/bin/freebayes [14:56:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:56:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:56:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:56:57] Found vcfuniq - /usr/local/bin/vcfuniq [14:56:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:56:57] Found gzip - /bin/gzip [14:56:57] Found vt - /usr/local/bin/vt [14:56:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:56:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:56:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:56:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:56:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:56:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:56:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:56:57] Please supply a reference FASTA/GBK/EMBL file with --reference
1[15:03:55] This is snippy 4.6.0
Show full stderr[15:03:55] This is snippy 4.6.0 [15:03:55] Written by Torsten Seemann [15:03:55] Obtained from https://github.com/tseemann/snippy [15:03:55] Detected operating system: linux [15:03:55] Enabling bundled linux tools. [15:03:55] Found bwa - /usr/local/bin/bwa [15:03:55] Found bcftools - /usr/local/bin/bcftools [15:03:55] Found samtools - /usr/local/bin/samtools [15:03:55] Found java - /usr/local/bin/java [15:03:55] Found snpEff - /usr/local/bin/snpEff [15:03:55] Found samclip - /usr/local/bin/samclip [15:03:55] Found seqtk - /usr/local/bin/seqtk [15:03:55] Found parallel - /usr/local/bin/parallel [15:03:55] Found freebayes - /usr/local/bin/freebayes [15:03:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [15:03:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [15:03:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [15:03:55] Found vcfuniq - /usr/local/bin/vcfuniq [15:03:55] Found vcffirstheader - /usr/local/bin/vcffirstheader [15:03:55] Found gzip - /bin/gzip [15:03:55] Found vt - /usr/local/bin/vt [15:03:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [15:03:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [15:03:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [15:03:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [15:03:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [15:03:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [15:03:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [15:03:56] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:45:36] This is snippy 4.6.0
Show full stderr[14:45:36] This is snippy 4.6.0 [14:45:36] Written by Torsten Seemann [14:45:36] Obtained from https://github.com/tseemann/snippy [14:45:36] Detected operating system: linux [14:45:36] Enabling bundled linux tools. [14:45:36] Found bwa - /usr/local/bin/bwa [14:45:36] Found bcftools - /usr/local/bin/bcftools [14:45:36] Found samtools - /usr/local/bin/samtools [14:45:36] Found java - /usr/local/bin/java [14:45:36] Found snpEff - /usr/local/bin/snpEff [14:45:36] Found samclip - /usr/local/bin/samclip [14:45:36] Found seqtk - /usr/local/bin/seqtk [14:45:36] Found parallel - /usr/local/bin/parallel [14:45:36] Found freebayes - /usr/local/bin/freebayes [14:45:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:45:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:45:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:45:36] Found vcfuniq - /usr/local/bin/vcfuniq [14:45:36] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:45:36] Found gzip - /bin/gzip [14:45:36] Found vt - /usr/local/bin/vt [14:45:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:45:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:45:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:45:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:45:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:45:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:45:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:45:37] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:45:42] This is snippy 4.6.0
Show full stderr[14:45:42] This is snippy 4.6.0 [14:45:42] Written by Torsten Seemann [14:45:42] Obtained from https://github.com/tseemann/snippy [14:45:42] Detected operating system: linux [14:45:42] Enabling bundled linux tools. [14:45:42] Found bwa - /usr/local/bin/bwa [14:45:42] Found bcftools - /usr/local/bin/bcftools [14:45:42] Found samtools - /usr/local/bin/samtools [14:45:42] Found java - /usr/local/bin/java [14:45:42] Found snpEff - /usr/local/bin/snpEff [14:45:42] Found samclip - /usr/local/bin/samclip [14:45:42] Found seqtk - /usr/local/bin/seqtk [14:45:42] Found parallel - /usr/local/bin/parallel [14:45:42] Found freebayes - /usr/local/bin/freebayes [14:45:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:45:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:45:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:45:42] Found vcfuniq - /usr/local/bin/vcfuniq [14:45:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:45:42] Found gzip - /bin/gzip [14:45:42] Found vt - /usr/local/bin/vt [14:45:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:45:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:45:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:45:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:45:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:45:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:45:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:45:43] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:46:04] This is snippy 4.6.0
Show full stderr[14:46:04] This is snippy 4.6.0 [14:46:04] Written by Torsten Seemann [14:46:04] Obtained from https://github.com/tseemann/snippy [14:46:04] Detected operating system: linux [14:46:04] Enabling bundled linux tools. [14:46:04] Found bwa - /usr/local/bin/bwa [14:46:04] Found bcftools - /usr/local/bin/bcftools [14:46:04] Found samtools - /usr/local/bin/samtools [14:46:04] Found java - /usr/local/bin/java [14:46:04] Found snpEff - /usr/local/bin/snpEff [14:46:04] Found samclip - /usr/local/bin/samclip [14:46:04] Found seqtk - /usr/local/bin/seqtk [14:46:04] Found parallel - /usr/local/bin/parallel [14:46:04] Found freebayes - /usr/local/bin/freebayes [14:46:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:46:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:46:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:46:04] Found vcfuniq - /usr/local/bin/vcfuniq [14:46:04] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:46:04] Found gzip - /bin/gzip [14:46:04] Found vt - /usr/local/bin/vt [14:46:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:46:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:46:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:46:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:46:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:46:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:46:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:46:05] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:46:00] This is snippy 4.6.0
Show full stderr[14:46:00] This is snippy 4.6.0 [14:46:00] Written by Torsten Seemann [14:46:00] Obtained from https://github.com/tseemann/snippy [14:46:00] Detected operating system: linux [14:46:00] Enabling bundled linux tools. [14:46:00] Found bwa - /usr/local/bin/bwa [14:46:00] Found bcftools - /usr/local/bin/bcftools [14:46:00] Found samtools - /usr/local/bin/samtools [14:46:00] Found java - /usr/local/bin/java [14:46:00] Found snpEff - /usr/local/bin/snpEff [14:46:00] Found samclip - /usr/local/bin/samclip [14:46:00] Found seqtk - /usr/local/bin/seqtk [14:46:00] Found parallel - /usr/local/bin/parallel [14:46:00] Found freebayes - /usr/local/bin/freebayes [14:46:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:46:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:46:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:46:00] Found vcfuniq - /usr/local/bin/vcfuniq [14:46:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:46:00] Found gzip - /bin/gzip [14:46:00] Found vt - /usr/local/bin/vt [14:46:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:46:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:46:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:46:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:46:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:46:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:46:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:46:01] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:46:22] This is snippy 4.6.0
Show full stderr[14:46:22] This is snippy 4.6.0 [14:46:22] Written by Torsten Seemann [14:46:22] Obtained from https://github.com/tseemann/snippy [14:46:22] Detected operating system: linux [14:46:22] Enabling bundled linux tools. [14:46:22] Found bwa - /usr/local/bin/bwa [14:46:22] Found bcftools - /usr/local/bin/bcftools [14:46:22] Found samtools - /usr/local/bin/samtools [14:46:22] Found java - /usr/local/bin/java [14:46:22] Found snpEff - /usr/local/bin/snpEff [14:46:22] Found samclip - /usr/local/bin/samclip [14:46:22] Found seqtk - /usr/local/bin/seqtk [14:46:22] Found parallel - /usr/local/bin/parallel [14:46:22] Found freebayes - /usr/local/bin/freebayes [14:46:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:46:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:46:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:46:22] Found vcfuniq - /usr/local/bin/vcfuniq [14:46:22] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:46:22] Found gzip - /bin/gzip [14:46:22] Found vt - /usr/local/bin/vt [14:46:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:46:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:46:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:46:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:46:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:46:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:46:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:46:23] Please supply a reference FASTA/GBK/EMBL file with --reference
1[15:09:00] This is snippy 4.6.0
Show full stderr[15:09:00] This is snippy 4.6.0 [15:09:00] Written by Torsten Seemann [15:09:00] Obtained from https://github.com/tseemann/snippy [15:09:00] Detected operating system: linux [15:09:00] Enabling bundled linux tools. [15:09:00] Found bwa - /usr/local/bin/bwa [15:09:00] Found bcftools - /usr/local/bin/bcftools [15:09:00] Found samtools - /usr/local/bin/samtools [15:09:00] Found java - /usr/local/bin/java [15:09:00] Found snpEff - /usr/local/bin/snpEff [15:09:00] Found samclip - /usr/local/bin/samclip [15:09:00] Found seqtk - /usr/local/bin/seqtk [15:09:00] Found parallel - /usr/local/bin/parallel [15:09:00] Found freebayes - /usr/local/bin/freebayes [15:09:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [15:09:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [15:09:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [15:09:00] Found vcfuniq - /usr/local/bin/vcfuniq [15:09:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [15:09:00] Found gzip - /bin/gzip [15:09:00] Found vt - /usr/local/bin/vt [15:09:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [15:09:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [15:09:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [15:09:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [15:09:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [15:09:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [15:09:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [15:09:03] Please supply a reference FASTA/GBK/EMBL file with --reference
1[15:14:53] This is snippy 4.6.0
Show full stderr[15:14:53] This is snippy 4.6.0 [15:14:53] Written by Torsten Seemann [15:14:53] Obtained from https://github.com/tseemann/snippy [15:14:53] Detected operating system: linux [15:14:53] Enabling bundled linux tools. [15:14:53] Found bwa - /usr/local/bin/bwa [15:14:53] Found bcftools - /usr/local/bin/bcftools [15:14:53] Found samtools - /usr/local/bin/samtools [15:14:53] Found java - /usr/local/bin/java [15:14:53] Found snpEff - /usr/local/bin/snpEff [15:14:53] Found samclip - /usr/local/bin/samclip [15:14:53] Found seqtk - /usr/local/bin/seqtk [15:14:53] Found parallel - /usr/local/bin/parallel [15:14:53] Found freebayes - /usr/local/bin/freebayes [15:14:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [15:14:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [15:14:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [15:14:53] Found vcfuniq - /usr/local/bin/vcfuniq [15:14:53] Found vcffirstheader - /usr/local/bin/vcffirstheader [15:14:53] Found gzip - /bin/gzip [15:14:53] Found vt - /usr/local/bin/vt [15:14:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [15:14:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [15:14:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [15:14:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [15:14:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [15:14:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [15:14:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [15:14:54] Please supply a reference FASTA/GBK/EMBL file with --reference
1[15:20:59] This is snippy 4.6.0
Show full stderr[15:20:59] This is snippy 4.6.0 [15:20:59] Written by Torsten Seemann [15:20:59] Obtained from https://github.com/tseemann/snippy [15:20:59] Detected operating system: linux [15:20:59] Enabling bundled linux tools. [15:20:59] Found bwa - /usr/local/bin/bwa [15:20:59] Found bcftools - /usr/local/bin/bcftools [15:20:59] Found samtools - /usr/local/bin/samtools [15:20:59] Found java - /usr/local/bin/java [15:20:59] Found snpEff - /usr/local/bin/snpEff [15:20:59] Found samclip - /usr/local/bin/samclip [15:20:59] Found seqtk - /usr/local/bin/seqtk [15:20:59] Found parallel - /usr/local/bin/parallel [15:20:59] Found freebayes - /usr/local/bin/freebayes [15:20:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [15:20:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [15:20:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [15:20:59] Found vcfuniq - /usr/local/bin/vcfuniq [15:20:59] Found vcffirstheader - /usr/local/bin/vcffirstheader [15:20:59] Found gzip - /bin/gzip [15:20:59] Found vt - /usr/local/bin/vt [15:20:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [15:20:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [15:20:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [15:20:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [15:20:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [15:21:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [15:21:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [15:21:00] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:46:06] This is snippy 4.6.0
Show full stderr[14:46:06] This is snippy 4.6.0 [14:46:06] Written by Torsten Seemann [14:46:06] Obtained from https://github.com/tseemann/snippy [14:46:06] Detected operating system: linux [14:46:06] Enabling bundled linux tools. [14:46:06] Found bwa - /usr/local/bin/bwa [14:46:06] Found bcftools - /usr/local/bin/bcftools [14:46:06] Found samtools - /usr/local/bin/samtools [14:46:06] Found java - /usr/local/bin/java [14:46:06] Found snpEff - /usr/local/bin/snpEff [14:46:06] Found samclip - /usr/local/bin/samclip [14:46:06] Found seqtk - /usr/local/bin/seqtk [14:46:06] Found parallel - /usr/local/bin/parallel [14:46:06] Found freebayes - /usr/local/bin/freebayes [14:46:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:46:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:46:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:46:06] Found vcfuniq - /usr/local/bin/vcfuniq [14:46:06] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:46:06] Found gzip - /bin/gzip [14:46:06] Found vt - /usr/local/bin/vt [14:46:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:46:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:46:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:46:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:46:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:46:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:46:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:46:07] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:58:21] This is snippy 4.6.0
Show full stderr[14:58:21] This is snippy 4.6.0 [14:58:21] Written by Torsten Seemann [14:58:21] Obtained from https://github.com/tseemann/snippy [14:58:21] Detected operating system: linux [14:58:21] Enabling bundled linux tools. [14:58:21] Found bwa - /usr/local/bin/bwa [14:58:21] Found bcftools - /usr/local/bin/bcftools [14:58:21] Found samtools - /usr/local/bin/samtools [14:58:21] Found java - /usr/local/bin/java [14:58:21] Found snpEff - /usr/local/bin/snpEff [14:58:21] Found samclip - /usr/local/bin/samclip [14:58:21] Found seqtk - /usr/local/bin/seqtk [14:58:21] Found parallel - /usr/local/bin/parallel [14:58:21] Found freebayes - /usr/local/bin/freebayes [14:58:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:58:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:58:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:58:21] Found vcfuniq - /usr/local/bin/vcfuniq [14:58:21] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:58:21] Found gzip - /bin/gzip [14:58:21] Found vt - /usr/local/bin/vt [14:58:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:58:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:58:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:58:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:58:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:58:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:58:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:58:24] Please supply a reference FASTA/GBK/EMBL file with --reference
1[15:04:25] This is snippy 4.6.0
Show full stderr[15:04:25] This is snippy 4.6.0 [15:04:25] Written by Torsten Seemann [15:04:25] Obtained from https://github.com/tseemann/snippy [15:04:25] Detected operating system: linux [15:04:25] Enabling bundled linux tools. [15:04:25] Found bwa - /usr/local/bin/bwa [15:04:25] Found bcftools - /usr/local/bin/bcftools [15:04:25] Found samtools - /usr/local/bin/samtools [15:04:25] Found java - /usr/local/bin/java [15:04:25] Found snpEff - /usr/local/bin/snpEff [15:04:25] Found samclip - /usr/local/bin/samclip [15:04:25] Found seqtk - /usr/local/bin/seqtk [15:04:25] Found parallel - /usr/local/bin/parallel [15:04:25] Found freebayes - /usr/local/bin/freebayes [15:04:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [15:04:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [15:04:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [15:04:25] Found vcfuniq - /usr/local/bin/vcfuniq [15:04:25] Found vcffirstheader - /usr/local/bin/vcffirstheader [15:04:25] Found gzip - /bin/gzip [15:04:25] Found vt - /usr/local/bin/vt [15:04:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [15:04:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [15:04:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [15:04:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [15:04:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [15:04:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [15:04:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [15:04:26] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:49:18] This is snippy 4.6.0
Show full stderr[14:49:18] This is snippy 4.6.0 [14:49:18] Written by Torsten Seemann [14:49:18] Obtained from https://github.com/tseemann/snippy [14:49:18] Detected operating system: linux [14:49:18] Enabling bundled linux tools. [14:49:18] Found bwa - /usr/local/bin/bwa [14:49:18] Found bcftools - /usr/local/bin/bcftools [14:49:18] Found samtools - /usr/local/bin/samtools [14:49:18] Found java - /usr/local/bin/java [14:49:18] Found snpEff - /usr/local/bin/snpEff [14:49:18] Found samclip - /usr/local/bin/samclip [14:49:18] Found seqtk - /usr/local/bin/seqtk [14:49:18] Found parallel - /usr/local/bin/parallel [14:49:18] Found freebayes - /usr/local/bin/freebayes [14:49:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:49:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:49:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:49:18] Found vcfuniq - /usr/local/bin/vcfuniq [14:49:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:49:18] Found gzip - /bin/gzip [14:49:18] Found vt - /usr/local/bin/vt [14:49:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:49:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:49:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:49:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:49:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:49:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:49:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:49:19] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:46:15] This is snippy 4.6.0
Show full stderr[14:46:15] This is snippy 4.6.0 [14:46:15] Written by Torsten Seemann [14:46:15] Obtained from https://github.com/tseemann/snippy [14:46:15] Detected operating system: linux [14:46:15] Enabling bundled linux tools. [14:46:15] Found bwa - /usr/local/bin/bwa [14:46:15] Found bcftools - /usr/local/bin/bcftools [14:46:15] Found samtools - /usr/local/bin/samtools [14:46:15] Found java - /usr/local/bin/java [14:46:15] Found snpEff - /usr/local/bin/snpEff [14:46:15] Found samclip - /usr/local/bin/samclip [14:46:15] Found seqtk - /usr/local/bin/seqtk [14:46:15] Found parallel - /usr/local/bin/parallel [14:46:15] Found freebayes - /usr/local/bin/freebayes [14:46:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:46:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:46:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:46:15] Found vcfuniq - /usr/local/bin/vcfuniq [14:46:15] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:46:15] Found gzip - /bin/gzip [14:46:15] Found vt - /usr/local/bin/vt [14:46:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:46:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:46:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:46:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:46:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:46:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:46:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:46:16] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:46:40] This is snippy 4.6.0
Show full stderr[14:46:40] This is snippy 4.6.0 [14:46:40] Written by Torsten Seemann [14:46:40] Obtained from https://github.com/tseemann/snippy [14:46:40] Detected operating system: linux [14:46:40] Enabling bundled linux tools. [14:46:40] Found bwa - /usr/local/bin/bwa [14:46:40] Found bcftools - /usr/local/bin/bcftools [14:46:40] Found samtools - /usr/local/bin/samtools [14:46:40] Found java - /usr/local/bin/java [14:46:40] Found snpEff - /usr/local/bin/snpEff [14:46:40] Found samclip - /usr/local/bin/samclip [14:46:40] Found seqtk - /usr/local/bin/seqtk [14:46:40] Found parallel - /usr/local/bin/parallel [14:46:40] Found freebayes - /usr/local/bin/freebayes [14:46:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:46:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:46:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:46:40] Found vcfuniq - /usr/local/bin/vcfuniq [14:46:40] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:46:40] Found gzip - /bin/gzip [14:46:40] Found vt - /usr/local/bin/vt [14:46:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:46:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:46:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:46:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:46:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:46:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:46:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:46:41] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:47:56] This is snippy 4.6.0
Show full stderr[14:47:56] This is snippy 4.6.0 [14:47:56] Written by Torsten Seemann [14:47:56] Obtained from https://github.com/tseemann/snippy [14:47:56] Detected operating system: linux [14:47:56] Enabling bundled linux tools. [14:47:56] Found bwa - /usr/local/bin/bwa [14:47:56] Found bcftools - /usr/local/bin/bcftools [14:47:56] Found samtools - /usr/local/bin/samtools [14:47:56] Found java - /usr/local/bin/java [14:47:56] Found snpEff - /usr/local/bin/snpEff [14:47:56] Found samclip - /usr/local/bin/samclip [14:47:56] Found seqtk - /usr/local/bin/seqtk [14:47:56] Found parallel - /usr/local/bin/parallel [14:47:56] Found freebayes - /usr/local/bin/freebayes [14:47:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:47:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:47:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:47:56] Found vcfuniq - /usr/local/bin/vcfuniq [14:47:56] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:47:56] Found gzip - /bin/gzip [14:47:56] Found vt - /usr/local/bin/vt [14:47:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:47:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:47:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:47:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:47:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:47:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:47:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:47:57] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:48:12] This is snippy 4.6.0
Show full stderr[14:48:12] This is snippy 4.6.0 [14:48:12] Written by Torsten Seemann [14:48:12] Obtained from https://github.com/tseemann/snippy [14:48:12] Detected operating system: linux [14:48:12] Enabling bundled linux tools. [14:48:12] Found bwa - /usr/local/bin/bwa [14:48:12] Found bcftools - /usr/local/bin/bcftools [14:48:12] Found samtools - /usr/local/bin/samtools [14:48:12] Found java - /usr/local/bin/java [14:48:12] Found snpEff - /usr/local/bin/snpEff [14:48:12] Found samclip - /usr/local/bin/samclip [14:48:12] Found seqtk - /usr/local/bin/seqtk [14:48:12] Found parallel - /usr/local/bin/parallel [14:48:12] Found freebayes - /usr/local/bin/freebayes [14:48:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:48:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:48:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:48:12] Found vcfuniq - /usr/local/bin/vcfuniq [14:48:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:48:12] Found gzip - /bin/gzip [14:48:12] Found vt - /usr/local/bin/vt [14:48:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:48:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:48:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:48:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:48:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:48:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:48:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:48:13] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:48:15] This is snippy 4.6.0
Show full stderr[14:48:15] This is snippy 4.6.0 [14:48:15] Written by Torsten Seemann [14:48:15] Obtained from https://github.com/tseemann/snippy [14:48:15] Detected operating system: linux [14:48:15] Enabling bundled linux tools. [14:48:15] Found bwa - /usr/local/bin/bwa [14:48:15] Found bcftools - /usr/local/bin/bcftools [14:48:15] Found samtools - /usr/local/bin/samtools [14:48:15] Found java - /usr/local/bin/java [14:48:15] Found snpEff - /usr/local/bin/snpEff [14:48:15] Found samclip - /usr/local/bin/samclip [14:48:15] Found seqtk - /usr/local/bin/seqtk [14:48:15] Found parallel - /usr/local/bin/parallel [14:48:15] Found freebayes - /usr/local/bin/freebayes [14:48:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:48:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:48:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:48:15] Found vcfuniq - /usr/local/bin/vcfuniq [14:48:15] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:48:15] Found gzip - /bin/gzip [14:48:15] Found vt - /usr/local/bin/vt [14:48:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:48:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:48:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:48:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:48:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:48:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:48:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:48:16] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:48:27] This is snippy 4.6.0
Show full stderr[14:48:27] This is snippy 4.6.0 [14:48:27] Written by Torsten Seemann [14:48:27] Obtained from https://github.com/tseemann/snippy [14:48:27] Detected operating system: linux [14:48:27] Enabling bundled linux tools. [14:48:27] Found bwa - /usr/local/bin/bwa [14:48:27] Found bcftools - /usr/local/bin/bcftools [14:48:27] Found samtools - /usr/local/bin/samtools [14:48:27] Found java - /usr/local/bin/java [14:48:27] Found snpEff - /usr/local/bin/snpEff [14:48:27] Found samclip - /usr/local/bin/samclip [14:48:27] Found seqtk - /usr/local/bin/seqtk [14:48:27] Found parallel - /usr/local/bin/parallel [14:48:27] Found freebayes - /usr/local/bin/freebayes [14:48:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:48:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:48:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:48:27] Found vcfuniq - /usr/local/bin/vcfuniq [14:48:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:48:27] Found gzip - /bin/gzip [14:48:27] Found vt - /usr/local/bin/vt [14:48:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:48:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:48:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:48:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:48:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:48:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:48:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:48:28] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:48:51] This is snippy 4.6.0
Show full stderr[14:48:51] This is snippy 4.6.0 [14:48:51] Written by Torsten Seemann [14:48:51] Obtained from https://github.com/tseemann/snippy [14:48:51] Detected operating system: linux [14:48:51] Enabling bundled linux tools. [14:48:51] Found bwa - /usr/local/bin/bwa [14:48:51] Found bcftools - /usr/local/bin/bcftools [14:48:51] Found samtools - /usr/local/bin/samtools [14:48:51] Found java - /usr/local/bin/java [14:48:51] Found snpEff - /usr/local/bin/snpEff [14:48:51] Found samclip - /usr/local/bin/samclip [14:48:51] Found seqtk - /usr/local/bin/seqtk [14:48:51] Found parallel - /usr/local/bin/parallel [14:48:51] Found freebayes - /usr/local/bin/freebayes [14:48:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:48:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:48:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:48:51] Found vcfuniq - /usr/local/bin/vcfuniq [14:48:51] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:48:51] Found gzip - /bin/gzip [14:48:51] Found vt - /usr/local/bin/vt [14:48:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:48:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:48:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:48:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:48:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:48:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:48:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:48:52] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:47:40] This is snippy 4.6.0
Show full stderr[14:47:40] This is snippy 4.6.0 [14:47:40] Written by Torsten Seemann [14:47:40] Obtained from https://github.com/tseemann/snippy [14:47:40] Detected operating system: linux [14:47:40] Enabling bundled linux tools. [14:47:40] Found bwa - /usr/local/bin/bwa [14:47:40] Found bcftools - /usr/local/bin/bcftools [14:47:40] Found samtools - /usr/local/bin/samtools [14:47:40] Found java - /usr/local/bin/java [14:47:40] Found snpEff - /usr/local/bin/snpEff [14:47:40] Found samclip - /usr/local/bin/samclip [14:47:40] Found seqtk - /usr/local/bin/seqtk [14:47:40] Found parallel - /usr/local/bin/parallel [14:47:40] Found freebayes - /usr/local/bin/freebayes [14:47:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:47:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:47:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:47:40] Found vcfuniq - /usr/local/bin/vcfuniq [14:47:40] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:47:40] Found gzip - /bin/gzip [14:47:40] Found vt - /usr/local/bin/vt [14:47:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:47:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:47:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:47:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:47:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:47:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:47:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:47:41] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:47:54] This is snippy 4.6.0
Show full stderr[14:47:54] This is snippy 4.6.0 [14:47:54] Written by Torsten Seemann [14:47:54] Obtained from https://github.com/tseemann/snippy [14:47:54] Detected operating system: linux [14:47:54] Enabling bundled linux tools. [14:47:54] Found bwa - /usr/local/bin/bwa [14:47:54] Found bcftools - /usr/local/bin/bcftools [14:47:54] Found samtools - /usr/local/bin/samtools [14:47:54] Found java - /usr/local/bin/java [14:47:54] Found snpEff - /usr/local/bin/snpEff [14:47:54] Found samclip - /usr/local/bin/samclip [14:47:54] Found seqtk - /usr/local/bin/seqtk [14:47:54] Found parallel - /usr/local/bin/parallel [14:47:54] Found freebayes - /usr/local/bin/freebayes [14:47:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:47:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:47:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:47:54] Found vcfuniq - /usr/local/bin/vcfuniq [14:47:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:47:54] Found gzip - /bin/gzip [14:47:54] Found vt - /usr/local/bin/vt [14:47:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:47:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:47:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:47:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:47:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:47:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:47:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:47:55] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:48:30] This is snippy 4.6.0
Show full stderr[14:48:30] This is snippy 4.6.0 [14:48:30] Written by Torsten Seemann [14:48:30] Obtained from https://github.com/tseemann/snippy [14:48:30] Detected operating system: linux [14:48:30] Enabling bundled linux tools. [14:48:30] Found bwa - /usr/local/bin/bwa [14:48:30] Found bcftools - /usr/local/bin/bcftools [14:48:30] Found samtools - /usr/local/bin/samtools [14:48:30] Found java - /usr/local/bin/java [14:48:30] Found snpEff - /usr/local/bin/snpEff [14:48:30] Found samclip - /usr/local/bin/samclip [14:48:30] Found seqtk - /usr/local/bin/seqtk [14:48:30] Found parallel - /usr/local/bin/parallel [14:48:30] Found freebayes - /usr/local/bin/freebayes [14:48:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:48:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:48:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:48:30] Found vcfuniq - /usr/local/bin/vcfuniq [14:48:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:48:30] Found gzip - /bin/gzip [14:48:30] Found vt - /usr/local/bin/vt [14:48:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:48:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:48:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:48:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:48:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:48:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:48:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:48:31] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:48:33] This is snippy 4.6.0
Show full stderr[14:48:33] This is snippy 4.6.0 [14:48:33] Written by Torsten Seemann [14:48:33] Obtained from https://github.com/tseemann/snippy [14:48:33] Detected operating system: linux [14:48:33] Enabling bundled linux tools. [14:48:33] Found bwa - /usr/local/bin/bwa [14:48:33] Found bcftools - /usr/local/bin/bcftools [14:48:33] Found samtools - /usr/local/bin/samtools [14:48:33] Found java - /usr/local/bin/java [14:48:33] Found snpEff - /usr/local/bin/snpEff [14:48:33] Found samclip - /usr/local/bin/samclip [14:48:33] Found seqtk - /usr/local/bin/seqtk [14:48:33] Found parallel - /usr/local/bin/parallel [14:48:33] Found freebayes - /usr/local/bin/freebayes [14:48:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:48:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:48:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:48:33] Found vcfuniq - /usr/local/bin/vcfuniq [14:48:33] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:48:33] Found gzip - /bin/gzip [14:48:33] Found vt - /usr/local/bin/vt [14:48:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:48:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:48:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:48:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:48:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:48:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:48:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:48:34] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:49:00] This is snippy 4.6.0
Show full stderr[14:49:00] This is snippy 4.6.0 [14:49:00] Written by Torsten Seemann [14:49:00] Obtained from https://github.com/tseemann/snippy [14:49:00] Detected operating system: linux [14:49:00] Enabling bundled linux tools. [14:49:00] Found bwa - /usr/local/bin/bwa [14:49:00] Found bcftools - /usr/local/bin/bcftools [14:49:00] Found samtools - /usr/local/bin/samtools [14:49:00] Found java - /usr/local/bin/java [14:49:00] Found snpEff - /usr/local/bin/snpEff [14:49:00] Found samclip - /usr/local/bin/samclip [14:49:00] Found seqtk - /usr/local/bin/seqtk [14:49:00] Found parallel - /usr/local/bin/parallel [14:49:00] Found freebayes - /usr/local/bin/freebayes [14:49:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:49:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:49:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:49:00] Found vcfuniq - /usr/local/bin/vcfuniq [14:49:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:49:00] Found gzip - /bin/gzip [14:49:00] Found vt - /usr/local/bin/vt [14:49:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:49:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:49:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:49:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:49:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:49:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:49:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:49:01] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:49:04] This is snippy 4.6.0
Show full stderr[14:49:04] This is snippy 4.6.0 [14:49:04] Written by Torsten Seemann [14:49:04] Obtained from https://github.com/tseemann/snippy [14:49:04] Detected operating system: linux [14:49:04] Enabling bundled linux tools. [14:49:04] Found bwa - /usr/local/bin/bwa [14:49:04] Found bcftools - /usr/local/bin/bcftools [14:49:04] Found samtools - /usr/local/bin/samtools [14:49:04] Found java - /usr/local/bin/java [14:49:04] Found snpEff - /usr/local/bin/snpEff [14:49:04] Found samclip - /usr/local/bin/samclip [14:49:04] Found seqtk - /usr/local/bin/seqtk [14:49:04] Found parallel - /usr/local/bin/parallel [14:49:04] Found freebayes - /usr/local/bin/freebayes [14:49:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:49:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:49:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:49:04] Found vcfuniq - /usr/local/bin/vcfuniq [14:49:04] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:49:04] Found gzip - /bin/gzip [14:49:04] Found vt - /usr/local/bin/vt [14:49:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:49:05] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:49:05] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:49:05] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:49:05] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:49:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:49:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:49:05] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:49:14] This is snippy 4.6.0
Show full stderr[14:49:14] This is snippy 4.6.0 [14:49:14] Written by Torsten Seemann [14:49:14] Obtained from https://github.com/tseemann/snippy [14:49:14] Detected operating system: linux [14:49:14] Enabling bundled linux tools. [14:49:14] Found bwa - /usr/local/bin/bwa [14:49:14] Found bcftools - /usr/local/bin/bcftools [14:49:14] Found samtools - /usr/local/bin/samtools [14:49:14] Found java - /usr/local/bin/java [14:49:14] Found snpEff - /usr/local/bin/snpEff [14:49:14] Found samclip - /usr/local/bin/samclip [14:49:14] Found seqtk - /usr/local/bin/seqtk [14:49:14] Found parallel - /usr/local/bin/parallel [14:49:14] Found freebayes - /usr/local/bin/freebayes [14:49:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:49:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:49:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:49:14] Found vcfuniq - /usr/local/bin/vcfuniq [14:49:14] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:49:14] Found gzip - /bin/gzip [14:49:14] Found vt - /usr/local/bin/vt [14:49:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:49:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:49:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:49:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:49:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:49:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:49:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:49:15] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:48:06] This is snippy 4.6.0
Show full stderr[14:48:06] This is snippy 4.6.0 [14:48:06] Written by Torsten Seemann [14:48:06] Obtained from https://github.com/tseemann/snippy [14:48:06] Detected operating system: linux [14:48:06] Enabling bundled linux tools. [14:48:06] Found bwa - /usr/local/bin/bwa [14:48:06] Found bcftools - /usr/local/bin/bcftools [14:48:06] Found samtools - /usr/local/bin/samtools [14:48:06] Found java - /usr/local/bin/java [14:48:06] Found snpEff - /usr/local/bin/snpEff [14:48:06] Found samclip - /usr/local/bin/samclip [14:48:06] Found seqtk - /usr/local/bin/seqtk [14:48:06] Found parallel - /usr/local/bin/parallel [14:48:06] Found freebayes - /usr/local/bin/freebayes [14:48:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:48:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:48:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:48:06] Found vcfuniq - /usr/local/bin/vcfuniq [14:48:06] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:48:06] Found gzip - /bin/gzip [14:48:06] Found vt - /usr/local/bin/vt [14:48:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:48:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:48:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:48:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:48:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:48:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:48:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:48:07] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:48:18] This is snippy 4.6.0
Show full stderr[14:48:18] This is snippy 4.6.0 [14:48:18] Written by Torsten Seemann [14:48:18] Obtained from https://github.com/tseemann/snippy [14:48:18] Detected operating system: linux [14:48:18] Enabling bundled linux tools. [14:48:18] Found bwa - /usr/local/bin/bwa [14:48:18] Found bcftools - /usr/local/bin/bcftools [14:48:18] Found samtools - /usr/local/bin/samtools [14:48:18] Found java - /usr/local/bin/java [14:48:18] Found snpEff - /usr/local/bin/snpEff [14:48:18] Found samclip - /usr/local/bin/samclip [14:48:18] Found seqtk - /usr/local/bin/seqtk [14:48:18] Found parallel - /usr/local/bin/parallel [14:48:18] Found freebayes - /usr/local/bin/freebayes [14:48:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:48:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:48:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:48:18] Found vcfuniq - /usr/local/bin/vcfuniq [14:48:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:48:18] Found gzip - /bin/gzip [14:48:18] Found vt - /usr/local/bin/vt [14:48:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:48:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:48:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:48:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:48:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:48:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:48:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:48:19] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:48:21] This is snippy 4.6.0
Show full stderr[14:48:21] This is snippy 4.6.0 [14:48:21] Written by Torsten Seemann [14:48:21] Obtained from https://github.com/tseemann/snippy [14:48:21] Detected operating system: linux [14:48:21] Enabling bundled linux tools. [14:48:21] Found bwa - /usr/local/bin/bwa [14:48:21] Found bcftools - /usr/local/bin/bcftools [14:48:21] Found samtools - /usr/local/bin/samtools [14:48:21] Found java - /usr/local/bin/java [14:48:21] Found snpEff - /usr/local/bin/snpEff [14:48:21] Found samclip - /usr/local/bin/samclip [14:48:21] Found seqtk - /usr/local/bin/seqtk [14:48:21] Found parallel - /usr/local/bin/parallel [14:48:21] Found freebayes - /usr/local/bin/freebayes [14:48:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:48:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:48:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:48:21] Found vcfuniq - /usr/local/bin/vcfuniq [14:48:21] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:48:21] Found gzip - /bin/gzip [14:48:21] Found vt - /usr/local/bin/vt [14:48:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:48:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:48:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:48:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:48:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:48:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:48:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:48:22] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:48:36] This is snippy 4.6.0
Show full stderr[14:48:36] This is snippy 4.6.0 [14:48:36] Written by Torsten Seemann [14:48:36] Obtained from https://github.com/tseemann/snippy [14:48:36] Detected operating system: linux [14:48:36] Enabling bundled linux tools. [14:48:36] Found bwa - /usr/local/bin/bwa [14:48:36] Found bcftools - /usr/local/bin/bcftools [14:48:36] Found samtools - /usr/local/bin/samtools [14:48:37] Found java - /usr/local/bin/java [14:48:37] Found snpEff - /usr/local/bin/snpEff [14:48:37] Found samclip - /usr/local/bin/samclip [14:48:37] Found seqtk - /usr/local/bin/seqtk [14:48:37] Found parallel - /usr/local/bin/parallel [14:48:37] Found freebayes - /usr/local/bin/freebayes [14:48:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:48:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:48:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:48:37] Found vcfuniq - /usr/local/bin/vcfuniq [14:48:37] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:48:37] Found gzip - /bin/gzip [14:48:37] Found vt - /usr/local/bin/vt [14:48:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:48:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:48:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:48:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:48:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:48:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:48:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:48:38] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:48:48] This is snippy 4.6.0
Show full stderr[14:48:48] This is snippy 4.6.0 [14:48:48] Written by Torsten Seemann [14:48:48] Obtained from https://github.com/tseemann/snippy [14:48:48] Detected operating system: linux [14:48:48] Enabling bundled linux tools. [14:48:48] Found bwa - /usr/local/bin/bwa [14:48:48] Found bcftools - /usr/local/bin/bcftools [14:48:48] Found samtools - /usr/local/bin/samtools [14:48:48] Found java - /usr/local/bin/java [14:48:49] Found snpEff - /usr/local/bin/snpEff [14:48:49] Found samclip - /usr/local/bin/samclip [14:48:49] Found seqtk - /usr/local/bin/seqtk [14:48:49] Found parallel - /usr/local/bin/parallel [14:48:49] Found freebayes - /usr/local/bin/freebayes [14:48:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:48:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:48:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:48:49] Found vcfuniq - /usr/local/bin/vcfuniq [14:48:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:48:49] Found gzip - /bin/gzip [14:48:49] Found vt - /usr/local/bin/vt [14:48:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:48:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:48:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:48:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:48:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:48:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:48:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:48:49] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:49:29] This is snippy 4.6.0
Show full stderr[14:49:29] This is snippy 4.6.0 [14:49:29] Written by Torsten Seemann [14:49:29] Obtained from https://github.com/tseemann/snippy [14:49:29] Detected operating system: linux [14:49:29] Enabling bundled linux tools. [14:49:29] Found bwa - /usr/local/bin/bwa [14:49:29] Found bcftools - /usr/local/bin/bcftools [14:49:29] Found samtools - /usr/local/bin/samtools [14:49:30] Found java - /usr/local/bin/java [14:49:30] Found snpEff - /usr/local/bin/snpEff [14:49:30] Found samclip - /usr/local/bin/samclip [14:49:30] Found seqtk - /usr/local/bin/seqtk [14:49:30] Found parallel - /usr/local/bin/parallel [14:49:30] Found freebayes - /usr/local/bin/freebayes [14:49:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:49:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:49:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:49:30] Found vcfuniq - /usr/local/bin/vcfuniq [14:49:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:49:30] Found gzip - /bin/gzip [14:49:30] Found vt - /usr/local/bin/vt [14:49:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:49:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:49:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:49:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:49:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:49:30] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:49:30] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:49:30] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:50:26] This is snippy 4.6.0
Show full stderr[14:50:26] This is snippy 4.6.0 [14:50:26] Written by Torsten Seemann [14:50:26] Obtained from https://github.com/tseemann/snippy [14:50:26] Detected operating system: linux [14:50:26] Enabling bundled linux tools. [14:50:26] Found bwa - /usr/local/bin/bwa [14:50:26] Found bcftools - /usr/local/bin/bcftools [14:50:26] Found samtools - /usr/local/bin/samtools [14:50:26] Found java - /usr/local/bin/java [14:50:26] Found snpEff - /usr/local/bin/snpEff [14:50:26] Found samclip - /usr/local/bin/samclip [14:50:26] Found seqtk - /usr/local/bin/seqtk [14:50:26] Found parallel - /usr/local/bin/parallel [14:50:26] Found freebayes - /usr/local/bin/freebayes [14:50:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:50:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:50:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:50:27] Found vcfuniq - /usr/local/bin/vcfuniq [14:50:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:50:27] Found gzip - /bin/gzip [14:50:27] Found vt - /usr/local/bin/vt [14:50:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:50:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:50:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:50:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:50:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:50:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:50:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:50:27] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:50:51] This is snippy 4.6.0
Show full stderr[14:50:51] This is snippy 4.6.0 [14:50:51] Written by Torsten Seemann [14:50:51] Obtained from https://github.com/tseemann/snippy [14:50:51] Detected operating system: linux [14:50:51] Enabling bundled linux tools. [14:50:51] Found bwa - /usr/local/bin/bwa [14:50:51] Found bcftools - /usr/local/bin/bcftools [14:50:51] Found samtools - /usr/local/bin/samtools [14:50:51] Found java - /usr/local/bin/java [14:50:51] Found snpEff - /usr/local/bin/snpEff [14:50:51] Found samclip - /usr/local/bin/samclip [14:50:51] Found seqtk - /usr/local/bin/seqtk [14:50:51] Found parallel - /usr/local/bin/parallel [14:50:51] Found freebayes - /usr/local/bin/freebayes [14:50:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:50:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:50:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:50:51] Found vcfuniq - /usr/local/bin/vcfuniq [14:50:51] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:50:51] Found gzip - /bin/gzip [14:50:51] Found vt - /usr/local/bin/vt [14:50:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:50:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:50:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:50:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:50:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:50:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:50:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:50:52] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:51:09] This is snippy 4.6.0
Show full stderr[14:51:09] This is snippy 4.6.0 [14:51:09] Written by Torsten Seemann [14:51:09] Obtained from https://github.com/tseemann/snippy [14:51:09] Detected operating system: linux [14:51:09] Enabling bundled linux tools. [14:51:09] Found bwa - /usr/local/bin/bwa [14:51:09] Found bcftools - /usr/local/bin/bcftools [14:51:09] Found samtools - /usr/local/bin/samtools [14:51:09] Found java - /usr/local/bin/java [14:51:09] Found snpEff - /usr/local/bin/snpEff [14:51:09] Found samclip - /usr/local/bin/samclip [14:51:09] Found seqtk - /usr/local/bin/seqtk [14:51:09] Found parallel - /usr/local/bin/parallel [14:51:09] Found freebayes - /usr/local/bin/freebayes [14:51:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:51:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:51:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:51:09] Found vcfuniq - /usr/local/bin/vcfuniq [14:51:09] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:51:09] Found gzip - /bin/gzip [14:51:09] Found vt - /usr/local/bin/vt [14:51:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:51:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:51:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:51:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:51:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:51:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:51:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:51:10] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:51:10] This is snippy 4.6.0
Show full stderr[14:51:10] This is snippy 4.6.0 [14:51:10] Written by Torsten Seemann [14:51:10] Obtained from https://github.com/tseemann/snippy [14:51:10] Detected operating system: linux [14:51:10] Enabling bundled linux tools. [14:51:10] Found bwa - /usr/local/bin/bwa [14:51:10] Found bcftools - /usr/local/bin/bcftools [14:51:10] Found samtools - /usr/local/bin/samtools [14:51:10] Found java - /usr/local/bin/java [14:51:10] Found snpEff - /usr/local/bin/snpEff [14:51:10] Found samclip - /usr/local/bin/samclip [14:51:10] Found seqtk - /usr/local/bin/seqtk [14:51:10] Found parallel - /usr/local/bin/parallel [14:51:10] Found freebayes - /usr/local/bin/freebayes [14:51:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:51:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:51:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:51:10] Found vcfuniq - /usr/local/bin/vcfuniq [14:51:10] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:51:10] Found gzip - /bin/gzip [14:51:10] Found vt - /usr/local/bin/vt [14:51:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:51:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:51:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:51:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:51:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:51:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:51:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:51:11] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:51:28] This is snippy 4.6.0
Show full stderr[14:51:28] This is snippy 4.6.0 [14:51:28] Written by Torsten Seemann [14:51:28] Obtained from https://github.com/tseemann/snippy [14:51:28] Detected operating system: linux [14:51:28] Enabling bundled linux tools. [14:51:28] Found bwa - /usr/local/bin/bwa [14:51:28] Found bcftools - /usr/local/bin/bcftools [14:51:29] Found samtools - /usr/local/bin/samtools [14:51:29] Found java - /usr/local/bin/java [14:51:29] Found snpEff - /usr/local/bin/snpEff [14:51:29] Found samclip - /usr/local/bin/samclip [14:51:29] Found seqtk - /usr/local/bin/seqtk [14:51:29] Found parallel - /usr/local/bin/parallel [14:51:29] Found freebayes - /usr/local/bin/freebayes [14:51:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:51:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:51:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:51:29] Found vcfuniq - /usr/local/bin/vcfuniq [14:51:29] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:51:29] Found gzip - /bin/gzip [14:51:29] Found vt - /usr/local/bin/vt [14:51:29] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:51:29] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:51:29] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:51:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:51:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:51:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:51:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:51:29] Please supply a reference FASTA/GBK/EMBL file with --reference
1[15:08:58] This is snippy 4.6.0
Show full stderr[15:08:58] This is snippy 4.6.0 [15:08:58] Written by Torsten Seemann [15:08:58] Obtained from https://github.com/tseemann/snippy [15:08:58] Detected operating system: linux [15:08:58] Enabling bundled linux tools. [15:08:58] Found bwa - /usr/local/bin/bwa [15:08:58] Found bcftools - /usr/local/bin/bcftools [15:08:58] Found samtools - /usr/local/bin/samtools [15:08:58] Found java - /usr/local/bin/java [15:08:58] Found snpEff - /usr/local/bin/snpEff [15:08:58] Found samclip - /usr/local/bin/samclip [15:08:58] Found seqtk - /usr/local/bin/seqtk [15:08:58] Found parallel - /usr/local/bin/parallel [15:08:58] Found freebayes - /usr/local/bin/freebayes [15:08:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [15:08:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [15:08:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [15:08:58] Found vcfuniq - /usr/local/bin/vcfuniq [15:08:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [15:08:58] Found gzip - /bin/gzip [15:08:58] Found vt - /usr/local/bin/vt [15:08:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [15:08:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [15:08:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [15:08:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [15:08:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [15:08:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [15:08:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [15:08:59] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:50:20] This is snippy 4.6.0
Show full stderr[14:50:20] This is snippy 4.6.0 [14:50:20] Written by Torsten Seemann [14:50:20] Obtained from https://github.com/tseemann/snippy [14:50:20] Detected operating system: linux [14:50:20] Enabling bundled linux tools. [14:50:20] Found bwa - /usr/local/bin/bwa [14:50:20] Found bcftools - /usr/local/bin/bcftools [14:50:20] Found samtools - /usr/local/bin/samtools [14:50:20] Found java - /usr/local/bin/java [14:50:21] Found snpEff - /usr/local/bin/snpEff [14:50:21] Found samclip - /usr/local/bin/samclip [14:50:21] Found seqtk - /usr/local/bin/seqtk [14:50:21] Found parallel - /usr/local/bin/parallel [14:50:21] Found freebayes - /usr/local/bin/freebayes [14:50:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:50:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:50:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:50:21] Found vcfuniq - /usr/local/bin/vcfuniq [14:50:21] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:50:21] Found gzip - /bin/gzip [14:50:21] Found vt - /usr/local/bin/vt [14:50:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:50:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:50:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:50:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:50:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:50:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:50:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:50:21] Please supply a reference FASTA/GBK/EMBL file with --reference
1[15:15:52] This is snippy 4.6.0
Show full stderr[15:15:52] This is snippy 4.6.0 [15:15:52] Written by Torsten Seemann [15:15:52] Obtained from https://github.com/tseemann/snippy [15:15:52] Detected operating system: linux [15:15:52] Enabling bundled linux tools. [15:15:52] Found bwa - /usr/local/bin/bwa [15:15:52] Found bcftools - /usr/local/bin/bcftools [15:15:52] Found samtools - /usr/local/bin/samtools [15:15:52] Found java - /usr/local/bin/java [15:15:52] Found snpEff - /usr/local/bin/snpEff [15:15:52] Found samclip - /usr/local/bin/samclip [15:15:52] Found seqtk - /usr/local/bin/seqtk [15:15:52] Found parallel - /usr/local/bin/parallel [15:15:52] Found freebayes - /usr/local/bin/freebayes [15:15:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [15:15:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [15:15:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [15:15:52] Found vcfuniq - /usr/local/bin/vcfuniq [15:15:52] Found vcffirstheader - /usr/local/bin/vcffirstheader [15:15:52] Found gzip - /bin/gzip [15:15:52] Found vt - /usr/local/bin/vt [15:15:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [15:15:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [15:15:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [15:15:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [15:15:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [15:15:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [15:15:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [15:15:53] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:50:39] This is snippy 4.6.0
Show full stderr[14:50:39] This is snippy 4.6.0 [14:50:39] Written by Torsten Seemann [14:50:39] Obtained from https://github.com/tseemann/snippy [14:50:39] Detected operating system: linux [14:50:39] Enabling bundled linux tools. [14:50:39] Found bwa - /usr/local/bin/bwa [14:50:39] Found bcftools - /usr/local/bin/bcftools [14:50:39] Found samtools - /usr/local/bin/samtools [14:50:39] Found java - /usr/local/bin/java [14:50:39] Found snpEff - /usr/local/bin/snpEff [14:50:39] Found samclip - /usr/local/bin/samclip [14:50:39] Found seqtk - /usr/local/bin/seqtk [14:50:39] Found parallel - /usr/local/bin/parallel [14:50:39] Found freebayes - /usr/local/bin/freebayes [14:50:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:50:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:50:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:50:39] Found vcfuniq - /usr/local/bin/vcfuniq [14:50:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:50:39] Found gzip - /bin/gzip [14:50:39] Found vt - /usr/local/bin/vt [14:50:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:50:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:50:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:50:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:50:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:50:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:50:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:50:40] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:50:40] This is snippy 4.6.0
Show full stderr[14:50:40] This is snippy 4.6.0 [14:50:40] Written by Torsten Seemann [14:50:40] Obtained from https://github.com/tseemann/snippy [14:50:40] Detected operating system: linux [14:50:40] Enabling bundled linux tools. [14:50:40] Found bwa - /usr/local/bin/bwa [14:50:40] Found bcftools - /usr/local/bin/bcftools [14:50:40] Found samtools - /usr/local/bin/samtools [14:50:40] Found java - /usr/local/bin/java [14:50:40] Found snpEff - /usr/local/bin/snpEff [14:50:40] Found samclip - /usr/local/bin/samclip [14:50:40] Found seqtk - /usr/local/bin/seqtk [14:50:40] Found parallel - /usr/local/bin/parallel [14:50:40] Found freebayes - /usr/local/bin/freebayes [14:50:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:50:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:50:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:50:40] Found vcfuniq - /usr/local/bin/vcfuniq [14:50:40] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:50:40] Found gzip - /bin/gzip [14:50:40] Found vt - /usr/local/bin/vt [14:50:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:50:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:50:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:50:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:50:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:50:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:50:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:50:41] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:51:26] This is snippy 4.6.0
Show full stderr[14:51:26] This is snippy 4.6.0 [14:51:26] Written by Torsten Seemann [14:51:26] Obtained from https://github.com/tseemann/snippy [14:51:26] Detected operating system: linux [14:51:26] Enabling bundled linux tools. [14:51:26] Found bwa - /usr/local/bin/bwa [14:51:26] Found bcftools - /usr/local/bin/bcftools [14:51:26] Found samtools - /usr/local/bin/samtools [14:51:26] Found java - /usr/local/bin/java [14:51:26] Found snpEff - /usr/local/bin/snpEff [14:51:26] Found samclip - /usr/local/bin/samclip [14:51:26] Found seqtk - /usr/local/bin/seqtk [14:51:26] Found parallel - /usr/local/bin/parallel [14:51:26] Found freebayes - /usr/local/bin/freebayes [14:51:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:51:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:51:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:51:26] Found vcfuniq - /usr/local/bin/vcfuniq [14:51:26] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:51:26] Found gzip - /bin/gzip [14:51:26] Found vt - /usr/local/bin/vt [14:51:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:51:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:51:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:51:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:51:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:51:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:51:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:51:26] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:52:09] This is snippy 4.6.0
Show full stderr[14:52:09] This is snippy 4.6.0 [14:52:09] Written by Torsten Seemann [14:52:09] Obtained from https://github.com/tseemann/snippy [14:52:09] Detected operating system: linux [14:52:09] Enabling bundled linux tools. [14:52:09] Found bwa - /usr/local/bin/bwa [14:52:09] Found bcftools - /usr/local/bin/bcftools [14:52:09] Found samtools - /usr/local/bin/samtools [14:52:09] Found java - /usr/local/bin/java [14:52:09] Found snpEff - /usr/local/bin/snpEff [14:52:09] Found samclip - /usr/local/bin/samclip [14:52:09] Found seqtk - /usr/local/bin/seqtk [14:52:09] Found parallel - /usr/local/bin/parallel [14:52:09] Found freebayes - /usr/local/bin/freebayes [14:52:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:52:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:52:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:52:09] Found vcfuniq - /usr/local/bin/vcfuniq [14:52:09] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:52:09] Found gzip - /bin/gzip [14:52:09] Found vt - /usr/local/bin/vt [14:52:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:52:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:52:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:52:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:52:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:52:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:52:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:52:10] Please supply a reference FASTA/GBK/EMBL file with --reference
1[15:16:26] This is snippy 4.6.0
Show full stderr[15:16:26] This is snippy 4.6.0 [15:16:26] Written by Torsten Seemann [15:16:26] Obtained from https://github.com/tseemann/snippy [15:16:26] Detected operating system: linux [15:16:26] Enabling bundled linux tools. [15:16:26] Found bwa - /usr/local/bin/bwa [15:16:26] Found bcftools - /usr/local/bin/bcftools [15:16:26] Found samtools - /usr/local/bin/samtools [15:16:26] Found java - /usr/local/bin/java [15:16:26] Found snpEff - /usr/local/bin/snpEff [15:16:26] Found samclip - /usr/local/bin/samclip [15:16:26] Found seqtk - /usr/local/bin/seqtk [15:16:26] Found parallel - /usr/local/bin/parallel [15:16:26] Found freebayes - /usr/local/bin/freebayes [15:16:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [15:16:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [15:16:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [15:16:26] Found vcfuniq - /usr/local/bin/vcfuniq [15:16:26] Found vcffirstheader - /usr/local/bin/vcffirstheader [15:16:26] Found gzip - /bin/gzip [15:16:26] Found vt - /usr/local/bin/vt [15:16:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [15:16:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [15:16:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [15:16:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [15:16:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [15:16:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [15:16:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [15:16:27] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:52:24] This is snippy 4.6.0
Show full stderr[14:52:24] This is snippy 4.6.0 [14:52:24] Written by Torsten Seemann [14:52:24] Obtained from https://github.com/tseemann/snippy [14:52:24] Detected operating system: linux [14:52:24] Enabling bundled linux tools. [14:52:24] Found bwa - /usr/local/bin/bwa [14:52:24] Found bcftools - /usr/local/bin/bcftools [14:52:24] Found samtools - /usr/local/bin/samtools [14:52:24] Found java - /usr/local/bin/java [14:52:24] Found snpEff - /usr/local/bin/snpEff [14:52:24] Found samclip - /usr/local/bin/samclip [14:52:24] Found seqtk - /usr/local/bin/seqtk [14:52:24] Found parallel - /usr/local/bin/parallel [14:52:24] Found freebayes - /usr/local/bin/freebayes [14:52:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:52:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:52:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:52:24] Found vcfuniq - /usr/local/bin/vcfuniq [14:52:24] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:52:24] Found gzip - /bin/gzip [14:52:24] Found vt - /usr/local/bin/vt [14:52:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:52:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:52:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:52:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:52:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:52:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:52:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:52:25] Please supply a reference FASTA/GBK/EMBL file with --reference
1[15:20:56] This is snippy 4.6.0
Show full stderr[15:20:56] This is snippy 4.6.0 [15:20:56] Written by Torsten Seemann [15:20:56] Obtained from https://github.com/tseemann/snippy [15:20:56] Detected operating system: linux [15:20:56] Enabling bundled linux tools. [15:20:56] Found bwa - /usr/local/bin/bwa [15:20:56] Found bcftools - /usr/local/bin/bcftools [15:20:56] Found samtools - /usr/local/bin/samtools [15:20:56] Found java - /usr/local/bin/java [15:20:56] Found snpEff - /usr/local/bin/snpEff [15:20:56] Found samclip - /usr/local/bin/samclip [15:20:56] Found seqtk - /usr/local/bin/seqtk [15:20:56] Found parallel - /usr/local/bin/parallel [15:20:56] Found freebayes - /usr/local/bin/freebayes [15:20:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [15:20:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [15:20:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [15:20:56] Found vcfuniq - /usr/local/bin/vcfuniq [15:20:56] Found vcffirstheader - /usr/local/bin/vcffirstheader [15:20:56] Found gzip - /bin/gzip [15:20:56] Found vt - /usr/local/bin/vt [15:20:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [15:20:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [15:20:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [15:20:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [15:20:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [15:20:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [15:20:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [15:20:57] Please supply a reference FASTA/GBK/EMBL file with --reference
1[15:22:26] This is snippy 4.6.0
Show full stderr[15:22:26] This is snippy 4.6.0 [15:22:26] Written by Torsten Seemann [15:22:26] Obtained from https://github.com/tseemann/snippy [15:22:26] Detected operating system: linux [15:22:26] Enabling bundled linux tools. [15:22:26] Found bwa - /usr/local/bin/bwa [15:22:26] Found bcftools - /usr/local/bin/bcftools [15:22:26] Found samtools - /usr/local/bin/samtools [15:22:26] Found java - /usr/local/bin/java [15:22:26] Found snpEff - /usr/local/bin/snpEff [15:22:26] Found samclip - /usr/local/bin/samclip [15:22:26] Found seqtk - /usr/local/bin/seqtk [15:22:26] Found parallel - /usr/local/bin/parallel [15:22:26] Found freebayes - /usr/local/bin/freebayes [15:22:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [15:22:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [15:22:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [15:22:26] Found vcfuniq - /usr/local/bin/vcfuniq [15:22:26] Found vcffirstheader - /usr/local/bin/vcffirstheader [15:22:26] Found gzip - /bin/gzip [15:22:26] Found vt - /usr/local/bin/vt [15:22:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [15:22:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [15:22:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [15:22:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [15:22:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [15:22:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [15:22:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [15:22:27] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:49:30] This is snippy 4.6.0
Show full stderr[14:49:30] This is snippy 4.6.0 [14:49:30] Written by Torsten Seemann [14:49:30] Obtained from https://github.com/tseemann/snippy [14:49:30] Detected operating system: linux [14:49:30] Enabling bundled linux tools. [14:49:30] Found bwa - /usr/local/bin/bwa [14:49:30] Found bcftools - /usr/local/bin/bcftools [14:49:30] Found samtools - /usr/local/bin/samtools [14:49:30] Found java - /usr/local/bin/java [14:49:30] Found snpEff - /usr/local/bin/snpEff [14:49:30] Found samclip - /usr/local/bin/samclip [14:49:30] Found seqtk - /usr/local/bin/seqtk [14:49:30] Found parallel - /usr/local/bin/parallel [14:49:30] Found freebayes - /usr/local/bin/freebayes [14:49:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:49:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:49:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:49:30] Found vcfuniq - /usr/local/bin/vcfuniq [14:49:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:49:30] Found gzip - /bin/gzip [14:49:30] Found vt - /usr/local/bin/vt [14:49:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:49:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:49:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:49:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:49:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:49:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:49:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:49:31] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:49:52] This is snippy 4.6.0
Show full stderr[14:49:52] This is snippy 4.6.0 [14:49:52] Written by Torsten Seemann [14:49:52] Obtained from https://github.com/tseemann/snippy [14:49:52] Detected operating system: linux [14:49:52] Enabling bundled linux tools. [14:49:52] Found bwa - /usr/local/bin/bwa [14:49:52] Found bcftools - /usr/local/bin/bcftools [14:49:52] Found samtools - /usr/local/bin/samtools [14:49:52] Found java - /usr/local/bin/java [14:49:52] Found snpEff - /usr/local/bin/snpEff [14:49:52] Found samclip - /usr/local/bin/samclip [14:49:52] Found seqtk - /usr/local/bin/seqtk [14:49:52] Found parallel - /usr/local/bin/parallel [14:49:52] Found freebayes - /usr/local/bin/freebayes [14:49:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:49:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:49:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:49:52] Found vcfuniq - /usr/local/bin/vcfuniq [14:49:52] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:49:52] Found gzip - /bin/gzip [14:49:52] Found vt - /usr/local/bin/vt [14:49:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:49:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:49:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:49:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:49:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:49:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:49:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:49:53] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:49:55] This is snippy 4.6.0
Show full stderr[14:49:55] This is snippy 4.6.0 [14:49:55] Written by Torsten Seemann [14:49:55] Obtained from https://github.com/tseemann/snippy [14:49:55] Detected operating system: linux [14:49:55] Enabling bundled linux tools. [14:49:55] Found bwa - /usr/local/bin/bwa [14:49:55] Found bcftools - /usr/local/bin/bcftools [14:49:55] Found samtools - /usr/local/bin/samtools [14:49:55] Found java - /usr/local/bin/java [14:49:55] Found snpEff - /usr/local/bin/snpEff [14:49:56] Found samclip - /usr/local/bin/samclip [14:49:56] Found seqtk - /usr/local/bin/seqtk [14:49:56] Found parallel - /usr/local/bin/parallel [14:49:56] Found freebayes - /usr/local/bin/freebayes [14:49:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:49:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:49:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:49:56] Found vcfuniq - /usr/local/bin/vcfuniq [14:49:56] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:49:56] Found gzip - /bin/gzip [14:49:56] Found vt - /usr/local/bin/vt [14:49:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:49:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:49:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:49:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:49:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:49:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:49:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:49:56] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:50:24] This is snippy 4.6.0
Show full stderr[14:50:24] This is snippy 4.6.0 [14:50:24] Written by Torsten Seemann [14:50:24] Obtained from https://github.com/tseemann/snippy [14:50:24] Detected operating system: linux [14:50:24] Enabling bundled linux tools. [14:50:24] Found bwa - /usr/local/bin/bwa [14:50:24] Found bcftools - /usr/local/bin/bcftools [14:50:24] Found samtools - /usr/local/bin/samtools [14:50:24] Found java - /usr/local/bin/java [14:50:24] Found snpEff - /usr/local/bin/snpEff [14:50:24] Found samclip - /usr/local/bin/samclip [14:50:24] Found seqtk - /usr/local/bin/seqtk [14:50:24] Found parallel - /usr/local/bin/parallel [14:50:24] Found freebayes - /usr/local/bin/freebayes [14:50:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:50:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:50:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:50:24] Found vcfuniq - /usr/local/bin/vcfuniq [14:50:24] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:50:24] Found gzip - /bin/gzip [14:50:24] Found vt - /usr/local/bin/vt [14:50:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:50:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:50:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:50:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:50:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:50:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:50:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:50:24] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:50:45] This is snippy 4.6.0
Show full stderr[14:50:45] This is snippy 4.6.0 [14:50:45] Written by Torsten Seemann [14:50:45] Obtained from https://github.com/tseemann/snippy [14:50:45] Detected operating system: linux [14:50:45] Enabling bundled linux tools. [14:50:45] Found bwa - /usr/local/bin/bwa [14:50:45] Found bcftools - /usr/local/bin/bcftools [14:50:45] Found samtools - /usr/local/bin/samtools [14:50:45] Found java - /usr/local/bin/java [14:50:45] Found snpEff - /usr/local/bin/snpEff [14:50:45] Found samclip - /usr/local/bin/samclip [14:50:45] Found seqtk - /usr/local/bin/seqtk [14:50:45] Found parallel - /usr/local/bin/parallel [14:50:45] Found freebayes - /usr/local/bin/freebayes [14:50:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:50:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:50:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:50:45] Found vcfuniq - /usr/local/bin/vcfuniq [14:50:45] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:50:45] Found gzip - /bin/gzip [14:50:45] Found vt - /usr/local/bin/vt [14:50:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:50:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:50:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:50:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:50:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:50:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:50:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:50:46] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:51:39] This is snippy 4.6.0
Show full stderr[14:51:39] This is snippy 4.6.0 [14:51:39] Written by Torsten Seemann [14:51:39] Obtained from https://github.com/tseemann/snippy [14:51:39] Detected operating system: linux [14:51:39] Enabling bundled linux tools. [14:51:39] Found bwa - /usr/local/bin/bwa [14:51:40] Found bcftools - /usr/local/bin/bcftools [14:51:40] Found samtools - /usr/local/bin/samtools [14:51:40] Found java - /usr/local/bin/java [14:51:40] Found snpEff - /usr/local/bin/snpEff [14:51:40] Found samclip - /usr/local/bin/samclip [14:51:40] Found seqtk - /usr/local/bin/seqtk [14:51:40] Found parallel - /usr/local/bin/parallel [14:51:40] Found freebayes - /usr/local/bin/freebayes [14:51:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:51:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:51:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:51:40] Found vcfuniq - /usr/local/bin/vcfuniq [14:51:40] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:51:40] Found gzip - /bin/gzip [14:51:40] Found vt - /usr/local/bin/vt [14:51:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:51:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:51:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:51:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:51:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:51:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:51:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:51:40] Please supply a reference FASTA/GBK/EMBL file with --reference
1[15:09:58] This is snippy 4.6.0
Show full stderr[15:09:58] This is snippy 4.6.0 [15:09:58] Written by Torsten Seemann [15:09:58] Obtained from https://github.com/tseemann/snippy [15:09:58] Detected operating system: linux [15:09:58] Enabling bundled linux tools. [15:09:58] Found bwa - /usr/local/bin/bwa [15:09:58] Found bcftools - /usr/local/bin/bcftools [15:09:58] Found samtools - /usr/local/bin/samtools [15:09:58] Found java - /usr/local/bin/java [15:09:58] Found snpEff - /usr/local/bin/snpEff [15:09:58] Found samclip - /usr/local/bin/samclip [15:09:58] Found seqtk - /usr/local/bin/seqtk [15:09:58] Found parallel - /usr/local/bin/parallel [15:09:58] Found freebayes - /usr/local/bin/freebayes [15:09:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [15:09:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [15:09:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [15:09:59] Found vcfuniq - /usr/local/bin/vcfuniq [15:09:59] Found vcffirstheader - /usr/local/bin/vcffirstheader [15:09:59] Found gzip - /bin/gzip [15:09:59] Found vt - /usr/local/bin/vt [15:09:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [15:09:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [15:09:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [15:09:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [15:09:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [15:09:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [15:09:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [15:09:59] Please supply a reference FASTA/GBK/EMBL file with --reference
1[15:10:25] This is snippy 4.6.0
Show full stderr[15:10:25] This is snippy 4.6.0 [15:10:25] Written by Torsten Seemann [15:10:25] Obtained from https://github.com/tseemann/snippy [15:10:25] Detected operating system: linux [15:10:25] Enabling bundled linux tools. [15:10:25] Found bwa - /usr/local/bin/bwa [15:10:25] Found bcftools - /usr/local/bin/bcftools [15:10:25] Found samtools - /usr/local/bin/samtools [15:10:25] Found java - /usr/local/bin/java [15:10:25] Found snpEff - /usr/local/bin/snpEff [15:10:25] Found samclip - /usr/local/bin/samclip [15:10:25] Found seqtk - /usr/local/bin/seqtk [15:10:25] Found parallel - /usr/local/bin/parallel [15:10:25] Found freebayes - /usr/local/bin/freebayes [15:10:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [15:10:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [15:10:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [15:10:25] Found vcfuniq - /usr/local/bin/vcfuniq [15:10:25] Found vcffirstheader - /usr/local/bin/vcffirstheader [15:10:25] Found gzip - /bin/gzip [15:10:25] Found vt - /usr/local/bin/vt [15:10:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [15:10:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [15:10:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [15:10:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [15:10:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [15:10:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [15:10:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [15:10:26] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:50:07] This is snippy 4.6.0
Show full stderr[14:50:07] This is snippy 4.6.0 [14:50:07] Written by Torsten Seemann [14:50:07] Obtained from https://github.com/tseemann/snippy [14:50:07] Detected operating system: linux [14:50:07] Enabling bundled linux tools. [14:50:07] Found bwa - /usr/local/bin/bwa [14:50:07] Found bcftools - /usr/local/bin/bcftools [14:50:08] Found samtools - /usr/local/bin/samtools [14:50:08] Found java - /usr/local/bin/java [14:50:08] Found snpEff - /usr/local/bin/snpEff [14:50:08] Found samclip - /usr/local/bin/samclip [14:50:08] Found seqtk - /usr/local/bin/seqtk [14:50:08] Found parallel - /usr/local/bin/parallel [14:50:08] Found freebayes - /usr/local/bin/freebayes [14:50:08] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:50:08] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:50:08] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:50:08] Found vcfuniq - /usr/local/bin/vcfuniq [14:50:08] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:50:08] Found gzip - /bin/gzip [14:50:08] Found vt - /usr/local/bin/vt [14:50:08] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:50:08] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:50:08] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:50:08] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:50:08] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:50:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:50:09] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:50:09] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:50:09] This is snippy 4.6.0
Show full stderr[14:50:09] This is snippy 4.6.0 [14:50:09] Written by Torsten Seemann [14:50:09] Obtained from https://github.com/tseemann/snippy [14:50:09] Detected operating system: linux [14:50:09] Enabling bundled linux tools. [14:50:09] Found bwa - /usr/local/bin/bwa [14:50:09] Found bcftools - /usr/local/bin/bcftools [14:50:09] Found samtools - /usr/local/bin/samtools [14:50:09] Found java - /usr/local/bin/java [14:50:09] Found snpEff - /usr/local/bin/snpEff [14:50:09] Found samclip - /usr/local/bin/samclip [14:50:09] Found seqtk - /usr/local/bin/seqtk [14:50:09] Found parallel - /usr/local/bin/parallel [14:50:09] Found freebayes - /usr/local/bin/freebayes [14:50:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:50:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:50:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:50:09] Found vcfuniq - /usr/local/bin/vcfuniq [14:50:09] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:50:09] Found gzip - /bin/gzip [14:50:09] Found vt - /usr/local/bin/vt [14:50:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:50:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:50:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:50:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:50:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:50:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:50:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:50:10] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:50:11] This is snippy 4.6.0
Show full stderr[14:50:11] This is snippy 4.6.0 [14:50:11] Written by Torsten Seemann [14:50:11] Obtained from https://github.com/tseemann/snippy [14:50:11] Detected operating system: linux [14:50:11] Enabling bundled linux tools. [14:50:11] Found bwa - /usr/local/bin/bwa [14:50:11] Found bcftools - /usr/local/bin/bcftools [14:50:11] Found samtools - /usr/local/bin/samtools [14:50:11] Found java - /usr/local/bin/java [14:50:11] Found snpEff - /usr/local/bin/snpEff [14:50:11] Found samclip - /usr/local/bin/samclip [14:50:11] Found seqtk - /usr/local/bin/seqtk [14:50:11] Found parallel - /usr/local/bin/parallel [14:50:11] Found freebayes - /usr/local/bin/freebayes [14:50:11] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:50:11] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:50:11] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:50:11] Found vcfuniq - /usr/local/bin/vcfuniq [14:50:11] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:50:11] Found gzip - /bin/gzip [14:50:11] Found vt - /usr/local/bin/vt [14:50:11] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:50:11] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:50:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:50:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:50:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:50:12] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:50:12] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:50:12] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:50:15] This is snippy 4.6.0
Show full stderr[14:50:15] This is snippy 4.6.0 [14:50:15] Written by Torsten Seemann [14:50:15] Obtained from https://github.com/tseemann/snippy [14:50:15] Detected operating system: linux [14:50:15] Enabling bundled linux tools. [14:50:15] Found bwa - /usr/local/bin/bwa [14:50:15] Found bcftools - /usr/local/bin/bcftools [14:50:15] Found samtools - /usr/local/bin/samtools [14:50:15] Found java - /usr/local/bin/java [14:50:15] Found snpEff - /usr/local/bin/snpEff [14:50:15] Found samclip - /usr/local/bin/samclip [14:50:15] Found seqtk - /usr/local/bin/seqtk [14:50:15] Found parallel - /usr/local/bin/parallel [14:50:15] Found freebayes - /usr/local/bin/freebayes [14:50:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:50:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:50:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:50:15] Found vcfuniq - /usr/local/bin/vcfuniq [14:50:15] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:50:15] Found gzip - /bin/gzip [14:50:15] Found vt - /usr/local/bin/vt [14:50:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:50:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:50:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:50:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:50:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:50:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:50:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:50:15] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:50:29] This is snippy 4.6.0
Show full stderr[14:50:29] This is snippy 4.6.0 [14:50:29] Written by Torsten Seemann [14:50:29] Obtained from https://github.com/tseemann/snippy [14:50:29] Detected operating system: linux [14:50:29] Enabling bundled linux tools. [14:50:29] Found bwa - /usr/local/bin/bwa [14:50:29] Found bcftools - /usr/local/bin/bcftools [14:50:29] Found samtools - /usr/local/bin/samtools [14:50:29] Found java - /usr/local/bin/java [14:50:29] Found snpEff - /usr/local/bin/snpEff [14:50:30] Found samclip - /usr/local/bin/samclip [14:50:30] Found seqtk - /usr/local/bin/seqtk [14:50:30] Found parallel - /usr/local/bin/parallel [14:50:30] Found freebayes - /usr/local/bin/freebayes [14:50:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:50:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:50:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:50:30] Found vcfuniq - /usr/local/bin/vcfuniq [14:50:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:50:30] Found gzip - /bin/gzip [14:50:30] Found vt - /usr/local/bin/vt [14:50:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:50:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:50:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:50:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:50:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:50:30] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:50:30] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:50:30] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:50:36] This is snippy 4.6.0
Show full stderr[14:50:36] This is snippy 4.6.0 [14:50:36] Written by Torsten Seemann [14:50:36] Obtained from https://github.com/tseemann/snippy [14:50:36] Detected operating system: linux [14:50:36] Enabling bundled linux tools. [14:50:36] Found bwa - /usr/local/bin/bwa [14:50:36] Found bcftools - /usr/local/bin/bcftools [14:50:36] Found samtools - /usr/local/bin/samtools [14:50:36] Found java - /usr/local/bin/java [14:50:36] Found snpEff - /usr/local/bin/snpEff [14:50:36] Found samclip - /usr/local/bin/samclip [14:50:36] Found seqtk - /usr/local/bin/seqtk [14:50:36] Found parallel - /usr/local/bin/parallel [14:50:36] Found freebayes - /usr/local/bin/freebayes [14:50:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:50:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:50:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:50:36] Found vcfuniq - /usr/local/bin/vcfuniq [14:50:36] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:50:36] Found gzip - /bin/gzip [14:50:36] Found vt - /usr/local/bin/vt [14:50:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:50:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:50:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:50:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:50:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:50:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:50:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:50:37] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:50:54] This is snippy 4.6.0
Show full stderr[14:50:54] This is snippy 4.6.0 [14:50:54] Written by Torsten Seemann [14:50:54] Obtained from https://github.com/tseemann/snippy [14:50:54] Detected operating system: linux [14:50:54] Enabling bundled linux tools. [14:50:54] Found bwa - /usr/local/bin/bwa [14:50:54] Found bcftools - /usr/local/bin/bcftools [14:50:54] Found samtools - /usr/local/bin/samtools [14:50:54] Found java - /usr/local/bin/java [14:50:54] Found snpEff - /usr/local/bin/snpEff [14:50:54] Found samclip - /usr/local/bin/samclip [14:50:54] Found seqtk - /usr/local/bin/seqtk [14:50:54] Found parallel - /usr/local/bin/parallel [14:50:54] Found freebayes - /usr/local/bin/freebayes [14:50:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:50:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:50:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:50:54] Found vcfuniq - /usr/local/bin/vcfuniq [14:50:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:50:54] Found gzip - /bin/gzip [14:50:54] Found vt - /usr/local/bin/vt [14:50:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:50:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:50:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:50:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:50:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:50:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:50:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:50:54] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:50:56] This is snippy 4.6.0
Show full stderr[14:50:56] This is snippy 4.6.0 [14:50:56] Written by Torsten Seemann [14:50:56] Obtained from https://github.com/tseemann/snippy [14:50:56] Detected operating system: linux [14:50:56] Enabling bundled linux tools. [14:50:56] Found bwa - /usr/local/bin/bwa [14:50:56] Found bcftools - /usr/local/bin/bcftools [14:50:56] Found samtools - /usr/local/bin/samtools [14:50:56] Found java - /usr/local/bin/java [14:50:56] Found snpEff - /usr/local/bin/snpEff [14:50:56] Found samclip - /usr/local/bin/samclip [14:50:56] Found seqtk - /usr/local/bin/seqtk [14:50:56] Found parallel - /usr/local/bin/parallel [14:50:56] Found freebayes - /usr/local/bin/freebayes [14:50:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:50:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:50:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:50:57] Found vcfuniq - /usr/local/bin/vcfuniq [14:50:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:50:57] Found gzip - /bin/gzip [14:50:57] Found vt - /usr/local/bin/vt [14:50:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:50:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:50:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:50:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:50:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:50:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:50:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:50:57] Please supply a reference FASTA/GBK/EMBL file with --reference
1[15:20:53] This is snippy 4.6.0
Show full stderr[15:20:53] This is snippy 4.6.0 [15:20:53] Written by Torsten Seemann [15:20:53] Obtained from https://github.com/tseemann/snippy [15:20:53] Detected operating system: linux [15:20:53] Enabling bundled linux tools. [15:20:53] Found bwa - /usr/local/bin/bwa [15:20:53] Found bcftools - /usr/local/bin/bcftools [15:20:53] Found samtools - /usr/local/bin/samtools [15:20:53] Found java - /usr/local/bin/java [15:20:53] Found snpEff - /usr/local/bin/snpEff [15:20:53] Found samclip - /usr/local/bin/samclip [15:20:53] Found seqtk - /usr/local/bin/seqtk [15:20:53] Found parallel - /usr/local/bin/parallel [15:20:53] Found freebayes - /usr/local/bin/freebayes [15:20:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [15:20:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [15:20:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [15:20:53] Found vcfuniq - /usr/local/bin/vcfuniq [15:20:53] Found vcffirstheader - /usr/local/bin/vcffirstheader [15:20:53] Found gzip - /bin/gzip [15:20:53] Found vt - /usr/local/bin/vt [15:20:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [15:20:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [15:20:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [15:20:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [15:20:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [15:20:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [15:20:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [15:20:53] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:52:05] This is snippy 4.6.0
Show full stderr[14:52:05] This is snippy 4.6.0 [14:52:05] Written by Torsten Seemann [14:52:05] Obtained from https://github.com/tseemann/snippy [14:52:05] Detected operating system: linux [14:52:05] Enabling bundled linux tools. [14:52:05] Found bwa - /usr/local/bin/bwa [14:52:05] Found bcftools - /usr/local/bin/bcftools [14:52:05] Found samtools - /usr/local/bin/samtools [14:52:05] Found java - /usr/local/bin/java [14:52:05] Found snpEff - /usr/local/bin/snpEff [14:52:05] Found samclip - /usr/local/bin/samclip [14:52:05] Found seqtk - /usr/local/bin/seqtk [14:52:05] Found parallel - /usr/local/bin/parallel [14:52:05] Found freebayes - /usr/local/bin/freebayes [14:52:05] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:52:05] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:52:05] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:52:05] Found vcfuniq - /usr/local/bin/vcfuniq [14:52:05] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:52:05] Found gzip - /bin/gzip [14:52:05] Found vt - /usr/local/bin/vt [14:52:05] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:52:05] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:52:05] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:52:05] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:52:05] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:52:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:52:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:52:05] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:52:20] This is snippy 4.6.0
Show full stderr[14:52:20] This is snippy 4.6.0 [14:52:20] Written by Torsten Seemann [14:52:20] Obtained from https://github.com/tseemann/snippy [14:52:20] Detected operating system: linux [14:52:20] Enabling bundled linux tools. [14:52:20] Found bwa - /usr/local/bin/bwa [14:52:20] Found bcftools - /usr/local/bin/bcftools [14:52:20] Found samtools - /usr/local/bin/samtools [14:52:20] Found java - /usr/local/bin/java [14:52:20] Found snpEff - /usr/local/bin/snpEff [14:52:20] Found samclip - /usr/local/bin/samclip [14:52:20] Found seqtk - /usr/local/bin/seqtk [14:52:20] Found parallel - /usr/local/bin/parallel [14:52:20] Found freebayes - /usr/local/bin/freebayes [14:52:20] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:52:20] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:52:20] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:52:20] Found vcfuniq - /usr/local/bin/vcfuniq [14:52:20] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:52:20] Found gzip - /bin/gzip [14:52:20] Found vt - /usr/local/bin/vt [14:52:20] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:52:20] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:52:20] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:52:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:52:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:52:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:52:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:52:21] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:52:50] This is snippy 4.6.0
Show full stderr[14:52:50] This is snippy 4.6.0 [14:52:50] Written by Torsten Seemann [14:52:50] Obtained from https://github.com/tseemann/snippy [14:52:50] Detected operating system: linux [14:52:50] Enabling bundled linux tools. [14:52:50] Found bwa - /usr/local/bin/bwa [14:52:50] Found bcftools - /usr/local/bin/bcftools [14:52:50] Found samtools - /usr/local/bin/samtools [14:52:50] Found java - /usr/local/bin/java [14:52:50] Found snpEff - /usr/local/bin/snpEff [14:52:50] Found samclip - /usr/local/bin/samclip [14:52:50] Found seqtk - /usr/local/bin/seqtk [14:52:50] Found parallel - /usr/local/bin/parallel [14:52:50] Found freebayes - /usr/local/bin/freebayes [14:52:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:52:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:52:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:52:50] Found vcfuniq - /usr/local/bin/vcfuniq [14:52:50] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:52:50] Found gzip - /bin/gzip [14:52:50] Found vt - /usr/local/bin/vt [14:52:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:52:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:52:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:52:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:52:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:52:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:52:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:52:51] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:53:04] This is snippy 4.6.0
Show full stderr[14:53:04] This is snippy 4.6.0 [14:53:04] Written by Torsten Seemann [14:53:04] Obtained from https://github.com/tseemann/snippy [14:53:04] Detected operating system: linux [14:53:04] Enabling bundled linux tools. [14:53:04] Found bwa - /usr/local/bin/bwa [14:53:04] Found bcftools - /usr/local/bin/bcftools [14:53:04] Found samtools - /usr/local/bin/samtools [14:53:04] Found java - /usr/local/bin/java [14:53:04] Found snpEff - /usr/local/bin/snpEff [14:53:04] Found samclip - /usr/local/bin/samclip [14:53:04] Found seqtk - /usr/local/bin/seqtk [14:53:04] Found parallel - /usr/local/bin/parallel [14:53:04] Found freebayes - /usr/local/bin/freebayes [14:53:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:53:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:53:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:53:04] Found vcfuniq - /usr/local/bin/vcfuniq [14:53:04] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:53:04] Found gzip - /bin/gzip [14:53:04] Found vt - /usr/local/bin/vt [14:53:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:53:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:53:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:53:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:53:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:53:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:53:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:53:05] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:53:09] This is snippy 4.6.0
Show full stderr[14:53:09] This is snippy 4.6.0 [14:53:09] Written by Torsten Seemann [14:53:09] Obtained from https://github.com/tseemann/snippy [14:53:09] Detected operating system: linux [14:53:09] Enabling bundled linux tools. [14:53:09] Found bwa - /usr/local/bin/bwa [14:53:09] Found bcftools - /usr/local/bin/bcftools [14:53:09] Found samtools - /usr/local/bin/samtools [14:53:09] Found java - /usr/local/bin/java [14:53:09] Found snpEff - /usr/local/bin/snpEff [14:53:09] Found samclip - /usr/local/bin/samclip [14:53:09] Found seqtk - /usr/local/bin/seqtk [14:53:09] Found parallel - /usr/local/bin/parallel [14:53:09] Found freebayes - /usr/local/bin/freebayes [14:53:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:53:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:53:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:53:09] Found vcfuniq - /usr/local/bin/vcfuniq [14:53:09] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:53:09] Found gzip - /bin/gzip [14:53:09] Found vt - /usr/local/bin/vt [14:53:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:53:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:53:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:53:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:53:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:53:09] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:53:09] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:53:09] Please supply a reference FASTA/GBK/EMBL file with --reference
1[15:21:55] This is snippy 4.6.0
Show full stderr[15:21:55] This is snippy 4.6.0 [15:21:55] Written by Torsten Seemann [15:21:55] Obtained from https://github.com/tseemann/snippy [15:21:55] Detected operating system: linux [15:21:55] Enabling bundled linux tools. [15:21:55] Found bwa - /usr/local/bin/bwa [15:21:55] Found bcftools - /usr/local/bin/bcftools [15:21:55] Found samtools - /usr/local/bin/samtools [15:21:55] Found java - /usr/local/bin/java [15:21:55] Found snpEff - /usr/local/bin/snpEff [15:21:55] Found samclip - /usr/local/bin/samclip [15:21:55] Found seqtk - /usr/local/bin/seqtk [15:21:55] Found parallel - /usr/local/bin/parallel [15:21:55] Found freebayes - /usr/local/bin/freebayes [15:21:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [15:21:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [15:21:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [15:21:55] Found vcfuniq - /usr/local/bin/vcfuniq [15:21:55] Found vcffirstheader - /usr/local/bin/vcffirstheader [15:21:55] Found gzip - /bin/gzip [15:21:55] Found vt - /usr/local/bin/vt [15:21:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [15:21:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [15:21:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [15:21:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [15:21:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [15:21:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [15:21:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [15:21:56] Please supply a reference FASTA/GBK/EMBL file with --reference
1[15:26:55] This is snippy 4.6.0
Show full stderr[15:26:55] This is snippy 4.6.0 [15:26:55] Written by Torsten Seemann [15:26:55] Obtained from https://github.com/tseemann/snippy [15:26:55] Detected operating system: linux [15:26:55] Enabling bundled linux tools. [15:26:55] Found bwa - /usr/local/bin/bwa [15:26:55] Found bcftools - /usr/local/bin/bcftools [15:26:55] Found samtools - /usr/local/bin/samtools [15:26:55] Found java - /usr/local/bin/java [15:26:55] Found snpEff - /usr/local/bin/snpEff [15:26:55] Found samclip - /usr/local/bin/samclip [15:26:55] Found seqtk - /usr/local/bin/seqtk [15:26:55] Found parallel - /usr/local/bin/parallel [15:26:55] Found freebayes - /usr/local/bin/freebayes [15:26:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [15:26:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [15:26:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [15:26:55] Found vcfuniq - /usr/local/bin/vcfuniq [15:26:55] Found vcffirstheader - /usr/local/bin/vcffirstheader [15:26:55] Found gzip - /bin/gzip [15:26:55] Found vt - /usr/local/bin/vt [15:26:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [15:26:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [15:26:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [15:26:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [15:26:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [15:26:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [15:26:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [15:26:56] Please supply a reference FASTA/GBK/EMBL file with --reference
1[15:26:58] This is snippy 4.6.0
Show full stderr[15:26:58] This is snippy 4.6.0 [15:26:58] Written by Torsten Seemann [15:26:58] Obtained from https://github.com/tseemann/snippy [15:26:58] Detected operating system: linux [15:26:58] Enabling bundled linux tools. [15:26:58] Found bwa - /usr/local/bin/bwa [15:26:58] Found bcftools - /usr/local/bin/bcftools [15:26:58] Found samtools - /usr/local/bin/samtools [15:26:58] Found java - /usr/local/bin/java [15:26:58] Found snpEff - /usr/local/bin/snpEff [15:26:58] Found samclip - /usr/local/bin/samclip [15:26:58] Found seqtk - /usr/local/bin/seqtk [15:26:58] Found parallel - /usr/local/bin/parallel [15:26:58] Found freebayes - /usr/local/bin/freebayes [15:26:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [15:26:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [15:26:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [15:26:58] Found vcfuniq - /usr/local/bin/vcfuniq [15:26:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [15:26:58] Found gzip - /bin/gzip [15:26:58] Found vt - /usr/local/bin/vt [15:26:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [15:26:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [15:26:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [15:26:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [15:26:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [15:26:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [15:26:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [15:26:59] Please supply a reference FASTA/GBK/EMBL file with --reference
1[15:27:54] This is snippy 4.6.0
Show full stderr[15:27:54] This is snippy 4.6.0 [15:27:54] Written by Torsten Seemann [15:27:54] Obtained from https://github.com/tseemann/snippy [15:27:54] Detected operating system: linux [15:27:54] Enabling bundled linux tools. [15:27:54] Found bwa - /usr/local/bin/bwa [15:27:54] Found bcftools - /usr/local/bin/bcftools [15:27:54] Found samtools - /usr/local/bin/samtools [15:27:54] Found java - /usr/local/bin/java [15:27:54] Found snpEff - /usr/local/bin/snpEff [15:27:54] Found samclip - /usr/local/bin/samclip [15:27:54] Found seqtk - /usr/local/bin/seqtk [15:27:54] Found parallel - /usr/local/bin/parallel [15:27:54] Found freebayes - /usr/local/bin/freebayes [15:27:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [15:27:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [15:27:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [15:27:54] Found vcfuniq - /usr/local/bin/vcfuniq [15:27:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [15:27:54] Found gzip - /bin/gzip [15:27:54] Found vt - /usr/local/bin/vt [15:27:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [15:27:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [15:27:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [15:27:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [15:27:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [15:27:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [15:27:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [15:27:55] Please supply a reference FASTA/GBK/EMBL file with --reference
1[15:28:25] This is snippy 4.6.0
Show full stderr[15:28:25] This is snippy 4.6.0 [15:28:25] Written by Torsten Seemann [15:28:25] Obtained from https://github.com/tseemann/snippy [15:28:25] Detected operating system: linux [15:28:25] Enabling bundled linux tools. [15:28:25] Found bwa - /usr/local/bin/bwa [15:28:25] Found bcftools - /usr/local/bin/bcftools [15:28:25] Found samtools - /usr/local/bin/samtools [15:28:25] Found java - /usr/local/bin/java [15:28:25] Found snpEff - /usr/local/bin/snpEff [15:28:25] Found samclip - /usr/local/bin/samclip [15:28:25] Found seqtk - /usr/local/bin/seqtk [15:28:25] Found parallel - /usr/local/bin/parallel [15:28:25] Found freebayes - /usr/local/bin/freebayes [15:28:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [15:28:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [15:28:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [15:28:25] Found vcfuniq - /usr/local/bin/vcfuniq [15:28:25] Found vcffirstheader - /usr/local/bin/vcffirstheader [15:28:25] Found gzip - /bin/gzip [15:28:25] Found vt - /usr/local/bin/vt [15:28:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [15:28:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [15:28:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [15:28:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [15:28:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [15:28:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [15:28:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [15:28:26] Please supply a reference FASTA/GBK/EMBL file with --reference
1[15:32:57] This is snippy 4.6.0
Show full stderr[15:32:57] This is snippy 4.6.0 [15:32:57] Written by Torsten Seemann [15:32:57] Obtained from https://github.com/tseemann/snippy [15:32:57] Detected operating system: linux [15:32:57] Enabling bundled linux tools. [15:32:57] Found bwa - /usr/local/bin/bwa [15:32:57] Found bcftools - /usr/local/bin/bcftools [15:32:57] Found samtools - /usr/local/bin/samtools [15:32:57] Found java - /usr/local/bin/java [15:32:57] Found snpEff - /usr/local/bin/snpEff [15:32:57] Found samclip - /usr/local/bin/samclip [15:32:57] Found seqtk - /usr/local/bin/seqtk [15:32:57] Found parallel - /usr/local/bin/parallel [15:32:57] Found freebayes - /usr/local/bin/freebayes [15:32:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [15:32:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [15:32:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [15:32:57] Found vcfuniq - /usr/local/bin/vcfuniq [15:32:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [15:32:57] Found gzip - /bin/gzip [15:32:57] Found vt - /usr/local/bin/vt [15:32:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [15:32:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [15:32:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [15:32:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [15:32:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [15:32:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [15:32:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [15:32:58] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:51:12] This is snippy 4.6.0
Show full stderr[14:51:12] This is snippy 4.6.0 [14:51:12] Written by Torsten Seemann [14:51:12] Obtained from https://github.com/tseemann/snippy [14:51:12] Detected operating system: linux [14:51:12] Enabling bundled linux tools. [14:51:12] Found bwa - /usr/local/bin/bwa [14:51:12] Found bcftools - /usr/local/bin/bcftools [14:51:12] Found samtools - /usr/local/bin/samtools [14:51:12] Found java - /usr/local/bin/java [14:51:12] Found snpEff - /usr/local/bin/snpEff [14:51:12] Found samclip - /usr/local/bin/samclip [14:51:12] Found seqtk - /usr/local/bin/seqtk [14:51:12] Found parallel - /usr/local/bin/parallel [14:51:12] Found freebayes - /usr/local/bin/freebayes [14:51:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:51:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:51:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:51:12] Found vcfuniq - /usr/local/bin/vcfuniq [14:51:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:51:12] Found gzip - /bin/gzip [14:51:12] Found vt - /usr/local/bin/vt [14:51:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:51:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:51:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:51:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:51:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:51:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:51:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:51:13] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:51:14] This is snippy 4.6.0
Show full stderr[14:51:14] This is snippy 4.6.0 [14:51:14] Written by Torsten Seemann [14:51:14] Obtained from https://github.com/tseemann/snippy [14:51:14] Detected operating system: linux [14:51:14] Enabling bundled linux tools. [14:51:14] Found bwa - /usr/local/bin/bwa [14:51:14] Found bcftools - /usr/local/bin/bcftools [14:51:14] Found samtools - /usr/local/bin/samtools [14:51:14] Found java - /usr/local/bin/java [14:51:14] Found snpEff - /usr/local/bin/snpEff [14:51:14] Found samclip - /usr/local/bin/samclip [14:51:14] Found seqtk - /usr/local/bin/seqtk [14:51:14] Found parallel - /usr/local/bin/parallel [14:51:14] Found freebayes - /usr/local/bin/freebayes [14:51:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:51:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:51:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:51:15] Found vcfuniq - /usr/local/bin/vcfuniq [14:51:15] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:51:15] Found gzip - /bin/gzip [14:51:15] Found vt - /usr/local/bin/vt [14:51:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:51:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:51:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:51:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:51:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:51:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:51:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:51:15] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:51:40] This is snippy 4.6.0
Show full stderr[14:51:40] This is snippy 4.6.0 [14:51:40] Written by Torsten Seemann [14:51:40] Obtained from https://github.com/tseemann/snippy [14:51:40] Detected operating system: linux [14:51:40] Enabling bundled linux tools. [14:51:40] Found bwa - /usr/local/bin/bwa [14:51:40] Found bcftools - /usr/local/bin/bcftools [14:51:40] Found samtools - /usr/local/bin/samtools [14:51:40] Found java - /usr/local/bin/java [14:51:40] Found snpEff - /usr/local/bin/snpEff [14:51:40] Found samclip - /usr/local/bin/samclip [14:51:40] Found seqtk - /usr/local/bin/seqtk [14:51:40] Found parallel - /usr/local/bin/parallel [14:51:40] Found freebayes - /usr/local/bin/freebayes [14:51:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:51:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:51:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:51:40] Found vcfuniq - /usr/local/bin/vcfuniq [14:51:40] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:51:40] Found gzip - /bin/gzip [14:51:40] Found vt - /usr/local/bin/vt [14:51:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:51:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:51:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:51:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:51:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:51:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:51:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:51:41] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:51:51] This is snippy 4.6.0
Show full stderr[14:51:51] This is snippy 4.6.0 [14:51:51] Written by Torsten Seemann [14:51:51] Obtained from https://github.com/tseemann/snippy [14:51:51] Detected operating system: linux [14:51:51] Enabling bundled linux tools. [14:51:51] Found bwa - /usr/local/bin/bwa [14:51:51] Found bcftools - /usr/local/bin/bcftools [14:51:51] Found samtools - /usr/local/bin/samtools [14:51:51] Found java - /usr/local/bin/java [14:51:51] Found snpEff - /usr/local/bin/snpEff [14:51:51] Found samclip - /usr/local/bin/samclip [14:51:51] Found seqtk - /usr/local/bin/seqtk [14:51:51] Found parallel - /usr/local/bin/parallel [14:51:51] Found freebayes - /usr/local/bin/freebayes [14:51:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:51:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:51:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:51:51] Found vcfuniq - /usr/local/bin/vcfuniq [14:51:51] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:51:51] Found gzip - /bin/gzip [14:51:51] Found vt - /usr/local/bin/vt [14:51:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:51:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:51:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:51:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:51:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:51:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:51:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:51:51] Please supply a reference FASTA/GBK/EMBL file with --reference
1[15:15:56] This is snippy 4.6.0
Show full stderr[15:15:56] This is snippy 4.6.0 [15:15:56] Written by Torsten Seemann [15:15:56] Obtained from https://github.com/tseemann/snippy [15:15:56] Detected operating system: linux [15:15:56] Enabling bundled linux tools. [15:15:56] Found bwa - /usr/local/bin/bwa [15:15:56] Found bcftools - /usr/local/bin/bcftools [15:15:56] Found samtools - /usr/local/bin/samtools [15:15:56] Found java - /usr/local/bin/java [15:15:56] Found snpEff - /usr/local/bin/snpEff [15:15:56] Found samclip - /usr/local/bin/samclip [15:15:56] Found seqtk - /usr/local/bin/seqtk [15:15:56] Found parallel - /usr/local/bin/parallel [15:15:56] Found freebayes - /usr/local/bin/freebayes [15:15:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [15:15:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [15:15:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [15:15:56] Found vcfuniq - /usr/local/bin/vcfuniq [15:15:56] Found vcffirstheader - /usr/local/bin/vcffirstheader [15:15:56] Found gzip - /bin/gzip [15:15:56] Found vt - /usr/local/bin/vt [15:15:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [15:15:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [15:15:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [15:15:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [15:15:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [15:15:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [15:15:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [15:15:57] Please supply a reference FASTA/GBK/EMBL file with --reference
1[15:32:26] This is snippy 4.6.0
Show full stderr[15:32:26] This is snippy 4.6.0 [15:32:26] Written by Torsten Seemann [15:32:26] Obtained from https://github.com/tseemann/snippy [15:32:26] Detected operating system: linux [15:32:26] Enabling bundled linux tools. [15:32:26] Found bwa - /usr/local/bin/bwa [15:32:26] Found bcftools - /usr/local/bin/bcftools [15:32:26] Found samtools - /usr/local/bin/samtools [15:32:26] Found java - /usr/local/bin/java [15:32:26] Found snpEff - /usr/local/bin/snpEff [15:32:26] Found samclip - /usr/local/bin/samclip [15:32:26] Found seqtk - /usr/local/bin/seqtk [15:32:26] Found parallel - /usr/local/bin/parallel [15:32:26] Found freebayes - /usr/local/bin/freebayes [15:32:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [15:32:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [15:32:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [15:32:26] Found vcfuniq - /usr/local/bin/vcfuniq [15:32:26] Found vcffirstheader - /usr/local/bin/vcffirstheader [15:32:26] Found gzip - /bin/gzip [15:32:26] Found vt - /usr/local/bin/vt [15:32:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [15:32:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [15:32:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [15:32:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [15:32:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [15:32:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [15:32:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [15:32:27] Please supply a reference FASTA/GBK/EMBL file with --reference
1[15:40:30] This is snippy 4.6.0
Show full stderr[15:40:30] This is snippy 4.6.0 [15:40:30] Written by Torsten Seemann [15:40:30] Obtained from https://github.com/tseemann/snippy [15:40:30] Detected operating system: linux [15:40:30] Enabling bundled linux tools. [15:40:30] Found bwa - /usr/local/bin/bwa [15:40:30] Found bcftools - /usr/local/bin/bcftools [15:40:30] Found samtools - /usr/local/bin/samtools [15:40:30] Found java - /usr/local/bin/java [15:40:30] Found snpEff - /usr/local/bin/snpEff [15:40:30] Found samclip - /usr/local/bin/samclip [15:40:30] Found seqtk - /usr/local/bin/seqtk [15:40:30] Found parallel - /usr/local/bin/parallel [15:40:30] Found freebayes - /usr/local/bin/freebayes [15:40:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [15:40:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [15:40:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [15:40:30] Found vcfuniq - /usr/local/bin/vcfuniq [15:40:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [15:40:30] Found gzip - /bin/gzip [15:40:30] Found vt - /usr/local/bin/vt [15:40:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [15:40:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [15:40:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [15:40:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [15:40:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [15:40:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [15:40:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [15:40:31] Please supply a reference FASTA/GBK/EMBL file with --reference
1[15:56:12] This is snippy 4.6.0
Show full stderr[15:56:12] This is snippy 4.6.0 [15:56:12] Written by Torsten Seemann [15:56:12] Obtained from https://github.com/tseemann/snippy [15:56:12] Detected operating system: linux [15:56:12] Enabling bundled linux tools. [15:56:12] Found bwa - /usr/local/bin/bwa [15:56:12] Found bcftools - /usr/local/bin/bcftools [15:56:12] Found samtools - /usr/local/bin/samtools [15:56:12] Found java - /usr/local/bin/java [15:56:12] Found snpEff - /usr/local/bin/snpEff [15:56:12] Found samclip - /usr/local/bin/samclip [15:56:12] Found seqtk - /usr/local/bin/seqtk [15:56:12] Found parallel - /usr/local/bin/parallel [15:56:12] Found freebayes - /usr/local/bin/freebayes [15:56:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [15:56:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [15:56:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [15:56:12] Found vcfuniq - /usr/local/bin/vcfuniq [15:56:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [15:56:12] Found gzip - /bin/gzip [15:56:12] Found vt - /usr/local/bin/vt [15:56:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [15:56:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [15:56:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [15:56:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [15:56:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [15:56:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [15:56:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [15:56:13] Please supply a reference FASTA/GBK/EMBL file with --reference
1[16:04:27] This is snippy 4.6.0
Show full stderr[16:04:27] This is snippy 4.6.0 [16:04:27] Written by Torsten Seemann [16:04:27] Obtained from https://github.com/tseemann/snippy [16:04:27] Detected operating system: linux [16:04:27] Enabling bundled linux tools. [16:04:27] Found bwa - /usr/local/bin/bwa [16:04:27] Found bcftools - /usr/local/bin/bcftools [16:04:27] Found samtools - /usr/local/bin/samtools [16:04:27] Found java - /usr/local/bin/java [16:04:27] Found snpEff - /usr/local/bin/snpEff [16:04:27] Found samclip - /usr/local/bin/samclip [16:04:27] Found seqtk - /usr/local/bin/seqtk [16:04:27] Found parallel - /usr/local/bin/parallel [16:04:27] Found freebayes - /usr/local/bin/freebayes [16:04:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [16:04:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [16:04:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [16:04:27] Found vcfuniq - /usr/local/bin/vcfuniq [16:04:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [16:04:27] Found gzip - /bin/gzip [16:04:27] Found vt - /usr/local/bin/vt [16:04:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [16:04:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [16:04:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [16:04:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [16:04:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [16:04:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [16:04:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [16:04:28] Please supply a reference FASTA/GBK/EMBL file with --reference
1[16:36:08] This is snippy 4.6.0
Show full stderr[16:36:08] This is snippy 4.6.0 [16:36:08] Written by Torsten Seemann [16:36:08] Obtained from https://github.com/tseemann/snippy [16:36:08] Detected operating system: linux [16:36:08] Enabling bundled linux tools. [16:36:08] Found bwa - /usr/local/bin/bwa [16:36:08] Found bcftools - /usr/local/bin/bcftools [16:36:08] Found samtools - /usr/local/bin/samtools [16:36:08] Found java - /usr/local/bin/java [16:36:08] Found snpEff - /usr/local/bin/snpEff [16:36:08] Found samclip - /usr/local/bin/samclip [16:36:08] Found seqtk - /usr/local/bin/seqtk [16:36:08] Found parallel - /usr/local/bin/parallel [16:36:08] Found freebayes - /usr/local/bin/freebayes [16:36:08] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [16:36:08] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [16:36:08] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [16:36:08] Found vcfuniq - /usr/local/bin/vcfuniq [16:36:08] Found vcffirstheader - /usr/local/bin/vcffirstheader [16:36:08] Found gzip - /bin/gzip [16:36:08] Found vt - /usr/local/bin/vt [16:36:08] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [16:36:08] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [16:36:08] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [16:36:08] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [16:36:08] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [16:36:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [16:36:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [16:36:08] Please supply a reference FASTA/GBK/EMBL file with --reference
1[16:43:56] This is snippy 4.6.0
Show full stderr[16:43:56] This is snippy 4.6.0 [16:43:56] Written by Torsten Seemann [16:43:56] Obtained from https://github.com/tseemann/snippy [16:43:56] Detected operating system: linux [16:43:56] Enabling bundled linux tools. [16:43:56] Found bwa - /usr/local/bin/bwa [16:43:56] Found bcftools - /usr/local/bin/bcftools [16:43:56] Found samtools - /usr/local/bin/samtools [16:43:56] Found java - /usr/local/bin/java [16:43:56] Found snpEff - /usr/local/bin/snpEff [16:43:56] Found samclip - /usr/local/bin/samclip [16:43:56] Found seqtk - /usr/local/bin/seqtk [16:43:56] Found parallel - /usr/local/bin/parallel [16:43:56] Found freebayes - /usr/local/bin/freebayes [16:43:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [16:43:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [16:43:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [16:43:56] Found vcfuniq - /usr/local/bin/vcfuniq [16:43:56] Found vcffirstheader - /usr/local/bin/vcffirstheader [16:43:56] Found gzip - /bin/gzip [16:43:56] Found vt - /usr/local/bin/vt [16:43:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [16:43:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [16:43:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [16:43:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [16:43:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [16:43:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [16:43:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [16:43:57] Please supply a reference FASTA/GBK/EMBL file with --reference
1[16:52:12] This is snippy 4.6.0
Show full stderr[16:52:12] This is snippy 4.6.0 [16:52:12] Written by Torsten Seemann [16:52:12] Obtained from https://github.com/tseemann/snippy [16:52:12] Detected operating system: linux [16:52:12] Enabling bundled linux tools. [16:52:12] Found bwa - /usr/local/bin/bwa [16:52:12] Found bcftools - /usr/local/bin/bcftools [16:52:12] Found samtools - /usr/local/bin/samtools [16:52:12] Found java - /usr/local/bin/java [16:52:12] Found snpEff - /usr/local/bin/snpEff [16:52:12] Found samclip - /usr/local/bin/samclip [16:52:12] Found seqtk - /usr/local/bin/seqtk [16:52:12] Found parallel - /usr/local/bin/parallel [16:52:12] Found freebayes - /usr/local/bin/freebayes [16:52:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [16:52:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [16:52:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [16:52:12] Found vcfuniq - /usr/local/bin/vcfuniq [16:52:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [16:52:12] Found gzip - /bin/gzip [16:52:12] Found vt - /usr/local/bin/vt [16:52:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [16:52:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [16:52:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [16:52:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [16:52:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [16:52:12] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [16:52:12] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [16:52:12] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:00:10] This is snippy 4.6.0
Show full stderr[17:00:10] This is snippy 4.6.0 [17:00:10] Written by Torsten Seemann [17:00:10] Obtained from https://github.com/tseemann/snippy [17:00:10] Detected operating system: linux [17:00:10] Enabling bundled linux tools. [17:00:10] Found bwa - /usr/local/bin/bwa [17:00:10] Found bcftools - /usr/local/bin/bcftools [17:00:10] Found samtools - /usr/local/bin/samtools [17:00:10] Found java - /usr/local/bin/java [17:00:10] Found snpEff - /usr/local/bin/snpEff [17:00:10] Found samclip - /usr/local/bin/samclip [17:00:10] Found seqtk - /usr/local/bin/seqtk [17:00:10] Found parallel - /usr/local/bin/parallel [17:00:10] Found freebayes - /usr/local/bin/freebayes [17:00:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:00:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:00:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:00:10] Found vcfuniq - /usr/local/bin/vcfuniq [17:00:10] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:00:10] Found gzip - /bin/gzip [17:00:10] Found vt - /usr/local/bin/vt [17:00:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:00:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:00:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:00:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:00:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:00:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:00:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:00:11] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:07:59] This is snippy 4.6.0
Show full stderr[17:07:59] This is snippy 4.6.0 [17:07:59] Written by Torsten Seemann [17:07:59] Obtained from https://github.com/tseemann/snippy [17:07:59] Detected operating system: linux [17:07:59] Enabling bundled linux tools. [17:07:59] Found bwa - /usr/local/bin/bwa [17:07:59] Found bcftools - /usr/local/bin/bcftools [17:07:59] Found samtools - /usr/local/bin/samtools [17:07:59] Found java - /usr/local/bin/java [17:07:59] Found snpEff - /usr/local/bin/snpEff [17:07:59] Found samclip - /usr/local/bin/samclip [17:07:59] Found seqtk - /usr/local/bin/seqtk [17:07:59] Found parallel - /usr/local/bin/parallel [17:07:59] Found freebayes - /usr/local/bin/freebayes [17:07:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:07:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:07:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:07:59] Found vcfuniq - /usr/local/bin/vcfuniq [17:07:59] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:07:59] Found gzip - /bin/gzip [17:07:59] Found vt - /usr/local/bin/vt [17:07:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:07:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:07:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:07:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:07:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:08:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:08:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:08:00] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:09:15] This is snippy 4.6.0
Show full stderr[17:09:15] This is snippy 4.6.0 [17:09:15] Written by Torsten Seemann [17:09:15] Obtained from https://github.com/tseemann/snippy [17:09:15] Detected operating system: linux [17:09:15] Enabling bundled linux tools. [17:09:15] Found bwa - /usr/local/bin/bwa [17:09:15] Found bcftools - /usr/local/bin/bcftools [17:09:15] Found samtools - /usr/local/bin/samtools [17:09:15] Found java - /usr/local/bin/java [17:09:15] Found snpEff - /usr/local/bin/snpEff [17:09:15] Found samclip - /usr/local/bin/samclip [17:09:15] Found seqtk - /usr/local/bin/seqtk [17:09:15] Found parallel - /usr/local/bin/parallel [17:09:15] Found freebayes - /usr/local/bin/freebayes [17:09:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:09:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:09:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:09:15] Found vcfuniq - /usr/local/bin/vcfuniq [17:09:15] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:09:15] Found gzip - /bin/gzip [17:09:15] Found vt - /usr/local/bin/vt [17:09:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:09:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:09:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:09:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:09:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:09:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:09:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:09:16] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:53:17] This is snippy 4.6.0
Show full stderr[17:53:17] This is snippy 4.6.0 [17:53:17] Written by Torsten Seemann [17:53:17] Obtained from https://github.com/tseemann/snippy [17:53:17] Detected operating system: linux [17:53:17] Enabling bundled linux tools. [17:53:17] Found bwa - /usr/local/bin/bwa [17:53:17] Found bcftools - /usr/local/bin/bcftools [17:53:17] Found samtools - /usr/local/bin/samtools [17:53:17] Found java - /usr/local/bin/java [17:53:17] Found snpEff - /usr/local/bin/snpEff [17:53:17] Found samclip - /usr/local/bin/samclip [17:53:17] Found seqtk - /usr/local/bin/seqtk [17:53:17] Found parallel - /usr/local/bin/parallel [17:53:17] Found freebayes - /usr/local/bin/freebayes [17:53:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:53:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:53:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:53:17] Found vcfuniq - /usr/local/bin/vcfuniq [17:53:17] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:53:17] Found gzip - /bin/gzip [17:53:17] Found vt - /usr/local/bin/vt [17:53:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:53:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:53:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:53:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:53:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:53:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:53:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:53:18] Please supply a reference FASTA/GBK/EMBL file with --reference
1[18:01:18] This is snippy 4.6.0
Show full stderr[18:01:18] This is snippy 4.6.0 [18:01:18] Written by Torsten Seemann [18:01:18] Obtained from https://github.com/tseemann/snippy [18:01:18] Detected operating system: linux [18:01:18] Enabling bundled linux tools. [18:01:18] Found bwa - /usr/local/bin/bwa [18:01:18] Found bcftools - /usr/local/bin/bcftools [18:01:18] Found samtools - /usr/local/bin/samtools [18:01:18] Found java - /usr/local/bin/java [18:01:18] Found snpEff - /usr/local/bin/snpEff [18:01:18] Found samclip - /usr/local/bin/samclip [18:01:18] Found seqtk - /usr/local/bin/seqtk [18:01:18] Found parallel - /usr/local/bin/parallel [18:01:18] Found freebayes - /usr/local/bin/freebayes [18:01:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [18:01:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [18:01:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [18:01:18] Found vcfuniq - /usr/local/bin/vcfuniq [18:01:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [18:01:18] Found gzip - /bin/gzip [18:01:18] Found vt - /usr/local/bin/vt [18:01:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [18:01:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [18:01:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [18:01:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [18:01:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [18:01:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [18:01:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [18:01:20] Please supply a reference FASTA/GBK/EMBL file with --reference
1[18:09:12] This is snippy 4.6.0
Show full stderr[18:09:12] This is snippy 4.6.0 [18:09:12] Written by Torsten Seemann [18:09:12] Obtained from https://github.com/tseemann/snippy [18:09:12] Detected operating system: linux [18:09:12] Enabling bundled linux tools. [18:09:12] Found bwa - /usr/local/bin/bwa [18:09:12] Found bcftools - /usr/local/bin/bcftools [18:09:12] Found samtools - /usr/local/bin/samtools [18:09:12] Found java - /usr/local/bin/java [18:09:12] Found snpEff - /usr/local/bin/snpEff [18:09:12] Found samclip - /usr/local/bin/samclip [18:09:12] Found seqtk - /usr/local/bin/seqtk [18:09:12] Found parallel - /usr/local/bin/parallel [18:09:12] Found freebayes - /usr/local/bin/freebayes [18:09:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [18:09:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [18:09:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [18:09:13] Found vcfuniq - /usr/local/bin/vcfuniq [18:09:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [18:09:13] Found gzip - /bin/gzip [18:09:13] Found vt - /usr/local/bin/vt [18:09:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [18:09:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [18:09:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [18:09:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [18:09:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [18:09:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [18:09:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [18:09:14] Please supply a reference FASTA/GBK/EMBL file with --reference
1[18:17:57] This is snippy 4.6.0
Show full stderr[18:17:57] This is snippy 4.6.0 [18:17:57] Written by Torsten Seemann [18:17:57] Obtained from https://github.com/tseemann/snippy [18:17:57] Detected operating system: linux [18:17:57] Enabling bundled linux tools. [18:17:57] Found bwa - /usr/local/bin/bwa [18:17:57] Found bcftools - /usr/local/bin/bcftools [18:17:57] Found samtools - /usr/local/bin/samtools [18:17:57] Found java - /usr/local/bin/java [18:17:57] Found snpEff - /usr/local/bin/snpEff [18:17:57] Found samclip - /usr/local/bin/samclip [18:17:57] Found seqtk - /usr/local/bin/seqtk [18:17:57] Found parallel - /usr/local/bin/parallel [18:17:57] Found freebayes - /usr/local/bin/freebayes [18:17:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [18:17:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [18:17:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [18:17:57] Found vcfuniq - /usr/local/bin/vcfuniq [18:17:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [18:17:57] Found gzip - /bin/gzip [18:17:57] Found vt - /usr/local/bin/vt [18:17:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [18:17:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [18:17:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [18:17:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [18:17:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [18:17:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [18:17:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [18:17:58] Please supply a reference FASTA/GBK/EMBL file with --reference
1[15:40:12] This is snippy 4.6.0
Show full stderr[15:40:12] This is snippy 4.6.0 [15:40:12] Written by Torsten Seemann [15:40:12] Obtained from https://github.com/tseemann/snippy [15:40:12] Detected operating system: linux [15:40:12] Enabling bundled linux tools. [15:40:12] Found bwa - /usr/local/bin/bwa [15:40:12] Found bcftools - /usr/local/bin/bcftools [15:40:12] Found samtools - /usr/local/bin/samtools [15:40:12] Found java - /usr/local/bin/java [15:40:12] Found snpEff - /usr/local/bin/snpEff [15:40:12] Found samclip - /usr/local/bin/samclip [15:40:12] Found seqtk - /usr/local/bin/seqtk [15:40:12] Found parallel - /usr/local/bin/parallel [15:40:12] Found freebayes - /usr/local/bin/freebayes [15:40:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [15:40:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [15:40:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [15:40:12] Found vcfuniq - /usr/local/bin/vcfuniq [15:40:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [15:40:12] Found gzip - /bin/gzip [15:40:12] Found vt - /usr/local/bin/vt [15:40:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [15:40:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [15:40:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [15:40:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [15:40:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [15:40:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [15:40:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [15:40:13] Please supply a reference FASTA/GBK/EMBL file with --reference
1[15:56:46] This is snippy 4.6.0
Show full stderr[15:56:46] This is snippy 4.6.0 [15:56:46] Written by Torsten Seemann [15:56:46] Obtained from https://github.com/tseemann/snippy [15:56:46] Detected operating system: linux [15:56:46] Enabling bundled linux tools. [15:56:46] Found bwa - /usr/local/bin/bwa [15:56:46] Found bcftools - /usr/local/bin/bcftools [15:56:46] Found samtools - /usr/local/bin/samtools [15:56:46] Found java - /usr/local/bin/java [15:56:46] Found snpEff - /usr/local/bin/snpEff [15:56:46] Found samclip - /usr/local/bin/samclip [15:56:46] Found seqtk - /usr/local/bin/seqtk [15:56:46] Found parallel - /usr/local/bin/parallel [15:56:46] Found freebayes - /usr/local/bin/freebayes [15:56:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [15:56:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [15:56:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [15:56:46] Found vcfuniq - /usr/local/bin/vcfuniq [15:56:46] Found vcffirstheader - /usr/local/bin/vcffirstheader [15:56:46] Found gzip - /bin/gzip [15:56:46] Found vt - /usr/local/bin/vt [15:56:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [15:56:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [15:56:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [15:56:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [15:56:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [15:56:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [15:56:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [15:56:48] Please supply a reference FASTA/GBK/EMBL file with --reference
1[16:28:18] This is snippy 4.6.0
Show full stderr[16:28:18] This is snippy 4.6.0 [16:28:18] Written by Torsten Seemann [16:28:18] Obtained from https://github.com/tseemann/snippy [16:28:18] Detected operating system: linux [16:28:18] Enabling bundled linux tools. [16:28:18] Found bwa - /usr/local/bin/bwa [16:28:18] Found bcftools - /usr/local/bin/bcftools [16:28:18] Found samtools - /usr/local/bin/samtools [16:28:18] Found java - /usr/local/bin/java [16:28:18] Found snpEff - /usr/local/bin/snpEff [16:28:18] Found samclip - /usr/local/bin/samclip [16:28:18] Found seqtk - /usr/local/bin/seqtk [16:28:18] Found parallel - /usr/local/bin/parallel [16:28:18] Found freebayes - /usr/local/bin/freebayes [16:28:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [16:28:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [16:28:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [16:28:18] Found vcfuniq - /usr/local/bin/vcfuniq [16:28:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [16:28:18] Found gzip - /bin/gzip [16:28:18] Found vt - /usr/local/bin/vt [16:28:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [16:28:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [16:28:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [16:28:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [16:28:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [16:28:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [16:28:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [16:28:19] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:26:47] This is snippy 4.6.0
Show full stderr[17:26:47] This is snippy 4.6.0 [17:26:47] Written by Torsten Seemann [17:26:47] Obtained from https://github.com/tseemann/snippy [17:26:47] Detected operating system: linux [17:26:47] Enabling bundled linux tools. [17:26:47] Found bwa - /usr/local/bin/bwa [17:26:47] Found bcftools - /usr/local/bin/bcftools [17:26:47] Found samtools - /usr/local/bin/samtools [17:26:47] Found java - /usr/local/bin/java [17:26:47] Found snpEff - /usr/local/bin/snpEff [17:26:47] Found samclip - /usr/local/bin/samclip [17:26:47] Found seqtk - /usr/local/bin/seqtk [17:26:47] Found parallel - /usr/local/bin/parallel [17:26:47] Found freebayes - /usr/local/bin/freebayes [17:26:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:26:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:26:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:26:47] Found vcfuniq - /usr/local/bin/vcfuniq [17:26:47] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:26:47] Found gzip - /bin/gzip [17:26:47] Found vt - /usr/local/bin/vt [17:26:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:26:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:26:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:26:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:26:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:26:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:26:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:26:48] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:34:48] This is snippy 4.6.0
Show full stderr[17:34:48] This is snippy 4.6.0 [17:34:48] Written by Torsten Seemann [17:34:48] Obtained from https://github.com/tseemann/snippy [17:34:48] Detected operating system: linux [17:34:48] Enabling bundled linux tools. [17:34:48] Found bwa - /usr/local/bin/bwa [17:34:48] Found bcftools - /usr/local/bin/bcftools [17:34:48] Found samtools - /usr/local/bin/samtools [17:34:48] Found java - /usr/local/bin/java [17:34:48] Found snpEff - /usr/local/bin/snpEff [17:34:48] Found samclip - /usr/local/bin/samclip [17:34:48] Found seqtk - /usr/local/bin/seqtk [17:34:48] Found parallel - /usr/local/bin/parallel [17:34:48] Found freebayes - /usr/local/bin/freebayes [17:34:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:34:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:34:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:34:48] Found vcfuniq - /usr/local/bin/vcfuniq [17:34:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:34:48] Found gzip - /bin/gzip [17:34:48] Found vt - /usr/local/bin/vt [17:34:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:34:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:34:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:34:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:34:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:34:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:34:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:34:51] Please supply a reference FASTA/GBK/EMBL file with --reference
1[21:20:53] This is snippy 4.6.0
Show full stderr[21:20:53] This is snippy 4.6.0 [21:20:53] Written by Torsten Seemann [21:20:53] Obtained from https://github.com/tseemann/snippy [21:20:53] Detected operating system: linux [21:20:53] Enabling bundled linux tools. [21:20:53] Found bwa - /usr/local/bin/bwa [21:20:53] Found bcftools - /usr/local/bin/bcftools [21:20:53] Found samtools - /usr/local/bin/samtools [21:20:53] Found java - /usr/local/bin/java [21:20:53] Found snpEff - /usr/local/bin/snpEff [21:20:53] Found samclip - /usr/local/bin/samclip [21:20:53] Found seqtk - /usr/local/bin/seqtk [21:20:53] Found parallel - /usr/local/bin/parallel [21:20:53] Found freebayes - /usr/local/bin/freebayes [21:20:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:20:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:20:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:20:53] Found vcfuniq - /usr/local/bin/vcfuniq [21:20:53] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:20:53] Found gzip - /bin/gzip [21:20:53] Found vt - /usr/local/bin/vt [21:20:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:20:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:20:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:20:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:20:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:20:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:20:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:20:54] Please supply a reference FASTA/GBK/EMBL file with --reference
1[22:03:34] This is snippy 4.6.0
Show full stderr[22:03:34] This is snippy 4.6.0 [22:03:34] Written by Torsten Seemann [22:03:34] Obtained from https://github.com/tseemann/snippy [22:03:34] Detected operating system: linux [22:03:34] Enabling bundled linux tools. [22:03:34] Found bwa - /usr/local/bin/bwa [22:03:34] Found bcftools - /usr/local/bin/bcftools [22:03:34] Found samtools - /usr/local/bin/samtools [22:03:34] Found java - /usr/local/bin/java [22:03:34] Found snpEff - /usr/local/bin/snpEff [22:03:34] Found samclip - /usr/local/bin/samclip [22:03:34] Found seqtk - /usr/local/bin/seqtk [22:03:34] Found parallel - /usr/local/bin/parallel [22:03:34] Found freebayes - /usr/local/bin/freebayes [22:03:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [22:03:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [22:03:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [22:03:34] Found vcfuniq - /usr/local/bin/vcfuniq [22:03:34] Found vcffirstheader - /usr/local/bin/vcffirstheader [22:03:34] Found gzip - /bin/gzip [22:03:34] Found vt - /usr/local/bin/vt [22:03:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [22:03:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [22:03:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [22:03:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [22:03:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [22:03:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [22:03:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [22:03:35] Please supply a reference FASTA/GBK/EMBL file with --reference
1[22:45:17] This is snippy 4.6.0
Show full stderr[22:45:17] This is snippy 4.6.0 [22:45:17] Written by Torsten Seemann [22:45:17] Obtained from https://github.com/tseemann/snippy [22:45:17] Detected operating system: linux [22:45:17] Enabling bundled linux tools. [22:45:17] Found bwa - /usr/local/bin/bwa [22:45:17] Found bcftools - /usr/local/bin/bcftools [22:45:17] Found samtools - /usr/local/bin/samtools [22:45:17] Found java - /usr/local/bin/java [22:45:17] Found snpEff - /usr/local/bin/snpEff [22:45:17] Found samclip - /usr/local/bin/samclip [22:45:17] Found seqtk - /usr/local/bin/seqtk [22:45:17] Found parallel - /usr/local/bin/parallel [22:45:17] Found freebayes - /usr/local/bin/freebayes [22:45:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [22:45:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [22:45:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [22:45:17] Found vcfuniq - /usr/local/bin/vcfuniq [22:45:17] Found vcffirstheader - /usr/local/bin/vcffirstheader [22:45:17] Found gzip - /bin/gzip [22:45:17] Found vt - /usr/local/bin/vt [22:45:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [22:45:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [22:45:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [22:45:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [22:45:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [22:45:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [22:45:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [22:45:18] Please supply a reference FASTA/GBK/EMBL file with --reference
1[22:53:18] This is snippy 4.6.0
Show full stderr[22:53:18] This is snippy 4.6.0 [22:53:18] Written by Torsten Seemann [22:53:18] Obtained from https://github.com/tseemann/snippy [22:53:18] Detected operating system: linux [22:53:18] Enabling bundled linux tools. [22:53:18] Found bwa - /usr/local/bin/bwa [22:53:18] Found bcftools - /usr/local/bin/bcftools [22:53:18] Found samtools - /usr/local/bin/samtools [22:53:18] Found java - /usr/local/bin/java [22:53:18] Found snpEff - /usr/local/bin/snpEff [22:53:18] Found samclip - /usr/local/bin/samclip [22:53:18] Found seqtk - /usr/local/bin/seqtk [22:53:18] Found parallel - /usr/local/bin/parallel [22:53:18] Found freebayes - /usr/local/bin/freebayes [22:53:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [22:53:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [22:53:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [22:53:18] Found vcfuniq - /usr/local/bin/vcfuniq [22:53:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [22:53:18] Found gzip - /bin/gzip [22:53:18] Found vt - /usr/local/bin/vt [22:53:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [22:53:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [22:53:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [22:53:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [22:53:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [22:53:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [22:53:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [22:53:18] Please supply a reference FASTA/GBK/EMBL file with --reference
1[23:01:02] This is snippy 4.6.0
Show full stderr[23:01:02] This is snippy 4.6.0 [23:01:02] Written by Torsten Seemann [23:01:02] Obtained from https://github.com/tseemann/snippy [23:01:02] Detected operating system: linux [23:01:02] Enabling bundled linux tools. [23:01:02] Found bwa - /usr/local/bin/bwa [23:01:02] Found bcftools - /usr/local/bin/bcftools [23:01:02] Found samtools - /usr/local/bin/samtools [23:01:02] Found java - /usr/local/bin/java [23:01:02] Found snpEff - /usr/local/bin/snpEff [23:01:02] Found samclip - /usr/local/bin/samclip [23:01:02] Found seqtk - /usr/local/bin/seqtk [23:01:02] Found parallel - /usr/local/bin/parallel [23:01:02] Found freebayes - /usr/local/bin/freebayes [23:01:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [23:01:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [23:01:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [23:01:02] Found vcfuniq - /usr/local/bin/vcfuniq [23:01:02] Found vcffirstheader - /usr/local/bin/vcffirstheader [23:01:02] Found gzip - /bin/gzip [23:01:02] Found vt - /usr/local/bin/vt [23:01:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [23:01:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [23:01:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [23:01:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [23:01:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [23:01:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [23:01:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [23:01:03] Please supply a reference FASTA/GBK/EMBL file with --reference
1[16:12:42] This is snippy 4.6.0
Show full stderr[16:12:42] This is snippy 4.6.0 [16:12:42] Written by Torsten Seemann [16:12:42] Obtained from https://github.com/tseemann/snippy [16:12:42] Detected operating system: linux [16:12:42] Enabling bundled linux tools. [16:12:42] Found bwa - /usr/local/bin/bwa [16:12:42] Found bcftools - /usr/local/bin/bcftools [16:12:42] Found samtools - /usr/local/bin/samtools [16:12:42] Found java - /usr/local/bin/java [16:12:42] Found snpEff - /usr/local/bin/snpEff [16:12:42] Found samclip - /usr/local/bin/samclip [16:12:42] Found seqtk - /usr/local/bin/seqtk [16:12:42] Found parallel - /usr/local/bin/parallel [16:12:42] Found freebayes - /usr/local/bin/freebayes [16:12:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [16:12:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [16:12:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [16:12:42] Found vcfuniq - /usr/local/bin/vcfuniq [16:12:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [16:12:42] Found gzip - /bin/gzip [16:12:42] Found vt - /usr/local/bin/vt [16:12:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [16:12:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [16:12:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [16:12:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [16:12:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [16:12:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [16:12:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [16:12:43] Please supply a reference FASTA/GBK/EMBL file with --reference
1[23:51:06] This is snippy 4.6.0
Show full stderr[23:51:06] This is snippy 4.6.0 [23:51:06] Written by Torsten Seemann [23:51:06] Obtained from https://github.com/tseemann/snippy [23:51:06] Detected operating system: linux [23:51:06] Enabling bundled linux tools. [23:51:06] Found bwa - /usr/local/bin/bwa [23:51:06] Found bcftools - /usr/local/bin/bcftools [23:51:06] Found samtools - /usr/local/bin/samtools [23:51:06] Found java - /usr/local/bin/java [23:51:06] Found snpEff - /usr/local/bin/snpEff [23:51:06] Found samclip - /usr/local/bin/samclip [23:51:06] Found seqtk - /usr/local/bin/seqtk [23:51:06] Found parallel - /usr/local/bin/parallel [23:51:06] Found freebayes - /usr/local/bin/freebayes [23:51:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [23:51:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [23:51:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [23:51:06] Found vcfuniq - /usr/local/bin/vcfuniq [23:51:06] Found vcffirstheader - /usr/local/bin/vcffirstheader [23:51:06] Found gzip - /bin/gzip [23:51:06] Found vt - /usr/local/bin/vt [23:51:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [23:51:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [23:51:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [23:51:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [23:51:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [23:51:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [23:51:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [23:51:06] Please supply a reference FASTA/GBK/EMBL file with --reference
1[21:20:27] This is snippy 4.6.0
Show full stderr[21:20:27] This is snippy 4.6.0 [21:20:27] Written by Torsten Seemann [21:20:27] Obtained from https://github.com/tseemann/snippy [21:20:27] Detected operating system: linux [21:20:27] Enabling bundled linux tools. [21:20:27] Found bwa - /usr/local/bin/bwa [21:20:27] Found bcftools - /usr/local/bin/bcftools [21:20:27] Found samtools - /usr/local/bin/samtools [21:20:27] Found java - /usr/local/bin/java [21:20:27] Found snpEff - /usr/local/bin/snpEff [21:20:27] Found samclip - /usr/local/bin/samclip [21:20:27] Found seqtk - /usr/local/bin/seqtk [21:20:27] Found parallel - /usr/local/bin/parallel [21:20:27] Found freebayes - /usr/local/bin/freebayes [21:20:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:20:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:20:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:20:27] Found vcfuniq - /usr/local/bin/vcfuniq [21:20:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:20:27] Found gzip - /bin/gzip [21:20:27] Found vt - /usr/local/bin/vt [21:20:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:20:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:20:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:20:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:20:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:20:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:20:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:20:28] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:08:08] This is snippy 4.6.0
Show full stderr[00:08:08] This is snippy 4.6.0 [00:08:08] Written by Torsten Seemann [00:08:08] Obtained from https://github.com/tseemann/snippy [00:08:08] Detected operating system: linux [00:08:08] Enabling bundled linux tools. [00:08:08] Found bwa - /usr/local/bin/bwa [00:08:08] Found bcftools - /usr/local/bin/bcftools [00:08:08] Found samtools - /usr/local/bin/samtools [00:08:08] Found java - /usr/local/bin/java [00:08:08] Found snpEff - /usr/local/bin/snpEff [00:08:08] Found samclip - /usr/local/bin/samclip [00:08:08] Found seqtk - /usr/local/bin/seqtk [00:08:08] Found parallel - /usr/local/bin/parallel [00:08:08] Found freebayes - /usr/local/bin/freebayes [00:08:08] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:08:08] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:08:08] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:08:08] Found vcfuniq - /usr/local/bin/vcfuniq [00:08:08] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:08:08] Found gzip - /bin/gzip [00:08:08] Found vt - /usr/local/bin/vt [00:08:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:08:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:08:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:08:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:08:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:08:09] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:08:09] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:08:09] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:44:18] This is snippy 4.6.0
Show full stderr[00:44:18] This is snippy 4.6.0 [00:44:18] Written by Torsten Seemann [00:44:18] Obtained from https://github.com/tseemann/snippy [00:44:18] Detected operating system: linux [00:44:18] Enabling bundled linux tools. [00:44:18] Found bwa - /usr/local/bin/bwa [00:44:18] Found bcftools - /usr/local/bin/bcftools [00:44:18] Found samtools - /usr/local/bin/samtools [00:44:18] Found java - /usr/local/bin/java [00:44:18] Found snpEff - /usr/local/bin/snpEff [00:44:18] Found samclip - /usr/local/bin/samclip [00:44:18] Found seqtk - /usr/local/bin/seqtk [00:44:18] Found parallel - /usr/local/bin/parallel [00:44:18] Found freebayes - /usr/local/bin/freebayes [00:44:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:44:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:44:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:44:18] Found vcfuniq - /usr/local/bin/vcfuniq [00:44:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:44:18] Found gzip - /bin/gzip [00:44:18] Found vt - /usr/local/bin/vt [00:44:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:44:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:44:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:44:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:44:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:44:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:44:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:44:19] Please supply a reference FASTA/GBK/EMBL file with --reference
1[15:48:20] This is snippy 4.6.0
Show full stderr[15:48:20] This is snippy 4.6.0 [15:48:20] Written by Torsten Seemann [15:48:20] Obtained from https://github.com/tseemann/snippy [15:48:20] Detected operating system: linux [15:48:20] Enabling bundled linux tools. [15:48:20] Found bwa - /usr/local/bin/bwa [15:48:20] Found bcftools - /usr/local/bin/bcftools [15:48:20] Found samtools - /usr/local/bin/samtools [15:48:20] Found java - /usr/local/bin/java [15:48:20] Found snpEff - /usr/local/bin/snpEff [15:48:20] Found samclip - /usr/local/bin/samclip [15:48:20] Found seqtk - /usr/local/bin/seqtk [15:48:20] Found parallel - /usr/local/bin/parallel [15:48:20] Found freebayes - /usr/local/bin/freebayes [15:48:20] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [15:48:20] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [15:48:20] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [15:48:20] Found vcfuniq - /usr/local/bin/vcfuniq [15:48:20] Found vcffirstheader - /usr/local/bin/vcffirstheader [15:48:20] Found gzip - /bin/gzip [15:48:20] Found vt - /usr/local/bin/vt [15:48:20] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [15:48:20] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [15:48:20] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [15:48:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [15:48:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [15:48:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [15:48:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [15:48:21] Please supply a reference FASTA/GBK/EMBL file with --reference
1[16:44:17] This is snippy 4.6.0
Show full stderr[16:44:17] This is snippy 4.6.0 [16:44:17] Written by Torsten Seemann [16:44:17] Obtained from https://github.com/tseemann/snippy [16:44:17] Detected operating system: linux [16:44:17] Enabling bundled linux tools. [16:44:17] Found bwa - /usr/local/bin/bwa [16:44:17] Found bcftools - /usr/local/bin/bcftools [16:44:17] Found samtools - /usr/local/bin/samtools [16:44:17] Found java - /usr/local/bin/java [16:44:17] Found snpEff - /usr/local/bin/snpEff [16:44:18] Found samclip - /usr/local/bin/samclip [16:44:18] Found seqtk - /usr/local/bin/seqtk [16:44:18] Found parallel - /usr/local/bin/parallel [16:44:18] Found freebayes - /usr/local/bin/freebayes [16:44:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [16:44:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [16:44:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [16:44:18] Found vcfuniq - /usr/local/bin/vcfuniq [16:44:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [16:44:18] Found gzip - /bin/gzip [16:44:18] Found vt - /usr/local/bin/vt [16:44:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [16:44:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [16:44:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [16:44:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [16:44:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [16:44:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [16:44:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [16:44:22] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:17:46] This is snippy 4.6.0
Show full stderr[17:17:46] This is snippy 4.6.0 [17:17:46] Written by Torsten Seemann [17:17:46] Obtained from https://github.com/tseemann/snippy [17:17:46] Detected operating system: linux [17:17:46] Enabling bundled linux tools. [17:17:46] Found bwa - /usr/local/bin/bwa [17:17:46] Found bcftools - /usr/local/bin/bcftools [17:17:46] Found samtools - /usr/local/bin/samtools [17:17:46] Found java - /usr/local/bin/java [17:17:46] Found snpEff - /usr/local/bin/snpEff [17:17:46] Found samclip - /usr/local/bin/samclip [17:17:46] Found seqtk - /usr/local/bin/seqtk [17:17:46] Found parallel - /usr/local/bin/parallel [17:17:46] Found freebayes - /usr/local/bin/freebayes [17:17:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:17:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:17:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:17:46] Found vcfuniq - /usr/local/bin/vcfuniq [17:17:46] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:17:46] Found gzip - /bin/gzip [17:17:46] Found vt - /usr/local/bin/vt [17:17:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:17:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:17:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:17:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:17:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:17:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:17:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:17:46] Please supply a reference FASTA/GBK/EMBL file with --reference
1[18:17:42] This is snippy 4.6.0
Show full stderr[18:17:42] This is snippy 4.6.0 [18:17:42] Written by Torsten Seemann [18:17:42] Obtained from https://github.com/tseemann/snippy [18:17:42] Detected operating system: linux [18:17:42] Enabling bundled linux tools. [18:17:42] Found bwa - /usr/local/bin/bwa [18:17:42] Found bcftools - /usr/local/bin/bcftools [18:17:42] Found samtools - /usr/local/bin/samtools [18:17:42] Found java - /usr/local/bin/java [18:17:42] Found snpEff - /usr/local/bin/snpEff [18:17:42] Found samclip - /usr/local/bin/samclip [18:17:42] Found seqtk - /usr/local/bin/seqtk [18:17:42] Found parallel - /usr/local/bin/parallel [18:17:42] Found freebayes - /usr/local/bin/freebayes [18:17:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [18:17:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [18:17:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [18:17:42] Found vcfuniq - /usr/local/bin/vcfuniq [18:17:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [18:17:42] Found gzip - /bin/gzip [18:17:42] Found vt - /usr/local/bin/vt [18:17:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [18:17:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [18:17:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [18:17:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [18:17:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [18:17:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [18:17:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [18:17:43] Please supply a reference FASTA/GBK/EMBL file with --reference
1[18:59:34] This is snippy 4.6.0
Show full stderr[18:59:34] This is snippy 4.6.0 [18:59:34] Written by Torsten Seemann [18:59:34] Obtained from https://github.com/tseemann/snippy [18:59:34] Detected operating system: linux [18:59:34] Enabling bundled linux tools. [18:59:34] Found bwa - /usr/local/bin/bwa [18:59:34] Found bcftools - /usr/local/bin/bcftools [18:59:34] Found samtools - /usr/local/bin/samtools [18:59:34] Found java - /usr/local/bin/java [18:59:34] Found snpEff - /usr/local/bin/snpEff [18:59:34] Found samclip - /usr/local/bin/samclip [18:59:34] Found seqtk - /usr/local/bin/seqtk [18:59:34] Found parallel - /usr/local/bin/parallel [18:59:34] Found freebayes - /usr/local/bin/freebayes [18:59:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [18:59:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [18:59:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [18:59:34] Found vcfuniq - /usr/local/bin/vcfuniq [18:59:34] Found vcffirstheader - /usr/local/bin/vcffirstheader [18:59:34] Found gzip - /bin/gzip [18:59:34] Found vt - /usr/local/bin/vt [18:59:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [18:59:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [18:59:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [18:59:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [18:59:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [18:59:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [18:59:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [18:59:35] Please supply a reference FASTA/GBK/EMBL file with --reference
1[19:33:18] This is snippy 4.6.0
Show full stderr[19:33:18] This is snippy 4.6.0 [19:33:18] Written by Torsten Seemann [19:33:18] Obtained from https://github.com/tseemann/snippy [19:33:18] Detected operating system: linux [19:33:18] Enabling bundled linux tools. [19:33:18] Found bwa - /usr/local/bin/bwa [19:33:18] Found bcftools - /usr/local/bin/bcftools [19:33:18] Found samtools - /usr/local/bin/samtools [19:33:18] Found java - /usr/local/bin/java [19:33:18] Found snpEff - /usr/local/bin/snpEff [19:33:18] Found samclip - /usr/local/bin/samclip [19:33:18] Found seqtk - /usr/local/bin/seqtk [19:33:18] Found parallel - /usr/local/bin/parallel [19:33:18] Found freebayes - /usr/local/bin/freebayes [19:33:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [19:33:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [19:33:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [19:33:18] Found vcfuniq - /usr/local/bin/vcfuniq [19:33:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [19:33:18] Found gzip - /bin/gzip [19:33:18] Found vt - /usr/local/bin/vt [19:33:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [19:33:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [19:33:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [19:33:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [19:33:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [19:33:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [19:33:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [19:33:19] Please supply a reference FASTA/GBK/EMBL file with --reference
1[19:49:12] This is snippy 4.6.0
Show full stderr[19:49:12] This is snippy 4.6.0 [19:49:12] Written by Torsten Seemann [19:49:12] Obtained from https://github.com/tseemann/snippy [19:49:12] Detected operating system: linux [19:49:12] Enabling bundled linux tools. [19:49:12] Found bwa - /usr/local/bin/bwa [19:49:12] Found bcftools - /usr/local/bin/bcftools [19:49:12] Found samtools - /usr/local/bin/samtools [19:49:12] Found java - /usr/local/bin/java [19:49:12] Found snpEff - /usr/local/bin/snpEff [19:49:12] Found samclip - /usr/local/bin/samclip [19:49:12] Found seqtk - /usr/local/bin/seqtk [19:49:12] Found parallel - /usr/local/bin/parallel [19:49:12] Found freebayes - /usr/local/bin/freebayes [19:49:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [19:49:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [19:49:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [19:49:12] Found vcfuniq - /usr/local/bin/vcfuniq [19:49:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [19:49:12] Found gzip - /bin/gzip [19:49:12] Found vt - /usr/local/bin/vt [19:49:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [19:49:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [19:49:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [19:49:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [19:49:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [19:49:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [19:49:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [19:49:13] Please supply a reference FASTA/GBK/EMBL file with --reference
1[21:12:18] This is snippy 4.6.0
Show full stderr[21:12:18] This is snippy 4.6.0 [21:12:18] Written by Torsten Seemann [21:12:18] Obtained from https://github.com/tseemann/snippy [21:12:18] Detected operating system: linux [21:12:18] Enabling bundled linux tools. [21:12:18] Found bwa - /usr/local/bin/bwa [21:12:18] Found bcftools - /usr/local/bin/bcftools [21:12:18] Found samtools - /usr/local/bin/samtools [21:12:18] Found java - /usr/local/bin/java [21:12:18] Found snpEff - /usr/local/bin/snpEff [21:12:18] Found samclip - /usr/local/bin/samclip [21:12:18] Found seqtk - /usr/local/bin/seqtk [21:12:18] Found parallel - /usr/local/bin/parallel [21:12:18] Found freebayes - /usr/local/bin/freebayes [21:12:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:12:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:12:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:12:18] Found vcfuniq - /usr/local/bin/vcfuniq [21:12:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:12:18] Found gzip - /bin/gzip [21:12:18] Found vt - /usr/local/bin/vt [21:12:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:12:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:12:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:12:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:12:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:12:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:12:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:12:20] Please supply a reference FASTA/GBK/EMBL file with --reference
1[21:22:17] This is snippy 4.6.0
Show full stderr[21:22:17] This is snippy 4.6.0 [21:22:17] Written by Torsten Seemann [21:22:17] Obtained from https://github.com/tseemann/snippy [21:22:17] Detected operating system: linux [21:22:17] Enabling bundled linux tools. [21:22:17] Found bwa - /usr/local/bin/bwa [21:22:17] Found bcftools - /usr/local/bin/bcftools [21:22:17] Found samtools - /usr/local/bin/samtools [21:22:17] Found java - /usr/local/bin/java [21:22:17] Found snpEff - /usr/local/bin/snpEff [21:22:17] Found samclip - /usr/local/bin/samclip [21:22:17] Found seqtk - /usr/local/bin/seqtk [21:22:17] Found parallel - /usr/local/bin/parallel [21:22:17] Found freebayes - /usr/local/bin/freebayes [21:22:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:22:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:22:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:22:17] Found vcfuniq - /usr/local/bin/vcfuniq [21:22:17] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:22:17] Found gzip - /bin/gzip [21:22:17] Found vt - /usr/local/bin/vt [21:22:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:22:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:22:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:22:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:22:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:22:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:22:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:22:18] Please supply a reference FASTA/GBK/EMBL file with --reference
1[22:03:47] This is snippy 4.6.0
Show full stderr[22:03:47] This is snippy 4.6.0 [22:03:47] Written by Torsten Seemann [22:03:47] Obtained from https://github.com/tseemann/snippy [22:03:47] Detected operating system: linux [22:03:47] Enabling bundled linux tools. [22:03:48] Found bwa - /usr/local/bin/bwa [22:03:48] Found bcftools - /usr/local/bin/bcftools [22:03:48] Found samtools - /usr/local/bin/samtools [22:03:48] Found java - /usr/local/bin/java [22:03:48] Found snpEff - /usr/local/bin/snpEff [22:03:48] Found samclip - /usr/local/bin/samclip [22:03:48] Found seqtk - /usr/local/bin/seqtk [22:03:48] Found parallel - /usr/local/bin/parallel [22:03:48] Found freebayes - /usr/local/bin/freebayes [22:03:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [22:03:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [22:03:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [22:03:48] Found vcfuniq - /usr/local/bin/vcfuniq [22:03:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [22:03:48] Found gzip - /bin/gzip [22:03:48] Found vt - /usr/local/bin/vt [22:03:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [22:03:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [22:03:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [22:03:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [22:03:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [22:03:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [22:03:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [22:03:48] Please supply a reference FASTA/GBK/EMBL file with --reference
1[22:28:15] This is snippy 4.6.0
Show full stderr[22:28:15] This is snippy 4.6.0 [22:28:15] Written by Torsten Seemann [22:28:15] Obtained from https://github.com/tseemann/snippy [22:28:15] Detected operating system: linux [22:28:15] Enabling bundled linux tools. [22:28:15] Found bwa - /usr/local/bin/bwa [22:28:15] Found bcftools - /usr/local/bin/bcftools [22:28:15] Found samtools - /usr/local/bin/samtools [22:28:15] Found java - /usr/local/bin/java [22:28:15] Found snpEff - /usr/local/bin/snpEff [22:28:15] Found samclip - /usr/local/bin/samclip [22:28:15] Found seqtk - /usr/local/bin/seqtk [22:28:15] Found parallel - /usr/local/bin/parallel [22:28:15] Found freebayes - /usr/local/bin/freebayes [22:28:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [22:28:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [22:28:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [22:28:15] Found vcfuniq - /usr/local/bin/vcfuniq [22:28:15] Found vcffirstheader - /usr/local/bin/vcffirstheader [22:28:15] Found gzip - /bin/gzip [22:28:15] Found vt - /usr/local/bin/vt [22:28:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [22:28:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [22:28:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [22:28:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [22:28:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [22:28:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [22:28:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [22:28:16] Please supply a reference FASTA/GBK/EMBL file with --reference
1[16:05:02] This is snippy 4.6.0
Show full stderr[16:05:02] This is snippy 4.6.0 [16:05:02] Written by Torsten Seemann [16:05:02] Obtained from https://github.com/tseemann/snippy [16:05:02] Detected operating system: linux [16:05:02] Enabling bundled linux tools. [16:05:02] Found bwa - /usr/local/bin/bwa [16:05:02] Found bcftools - /usr/local/bin/bcftools [16:05:02] Found samtools - /usr/local/bin/samtools [16:05:02] Found java - /usr/local/bin/java [16:05:02] Found snpEff - /usr/local/bin/snpEff [16:05:02] Found samclip - /usr/local/bin/samclip [16:05:02] Found seqtk - /usr/local/bin/seqtk [16:05:02] Found parallel - /usr/local/bin/parallel [16:05:02] Found freebayes - /usr/local/bin/freebayes [16:05:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [16:05:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [16:05:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [16:05:02] Found vcfuniq - /usr/local/bin/vcfuniq [16:05:02] Found vcffirstheader - /usr/local/bin/vcffirstheader [16:05:02] Found gzip - /bin/gzip [16:05:02] Found vt - /usr/local/bin/vt [16:05:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [16:05:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [16:05:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [16:05:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [16:05:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [16:05:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [16:05:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [16:05:03] Please supply a reference FASTA/GBK/EMBL file with --reference
1[16:20:33] This is snippy 4.6.0
Show full stderr[16:20:33] This is snippy 4.6.0 [16:20:33] Written by Torsten Seemann [16:20:33] Obtained from https://github.com/tseemann/snippy [16:20:33] Detected operating system: linux [16:20:33] Enabling bundled linux tools. [16:20:33] Found bwa - /usr/local/bin/bwa [16:20:33] Found bcftools - /usr/local/bin/bcftools [16:20:33] Found samtools - /usr/local/bin/samtools [16:20:33] Found java - /usr/local/bin/java [16:20:33] Found snpEff - /usr/local/bin/snpEff [16:20:33] Found samclip - /usr/local/bin/samclip [16:20:33] Found seqtk - /usr/local/bin/seqtk [16:20:33] Found parallel - /usr/local/bin/parallel [16:20:33] Found freebayes - /usr/local/bin/freebayes [16:20:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [16:20:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [16:20:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [16:20:33] Found vcfuniq - /usr/local/bin/vcfuniq [16:20:33] Found vcffirstheader - /usr/local/bin/vcffirstheader [16:20:33] Found gzip - /bin/gzip [16:20:33] Found vt - /usr/local/bin/vt [16:20:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [16:20:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [16:20:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [16:20:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [16:20:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [16:20:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [16:20:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [16:20:35] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:26:01] This is snippy 4.6.0
Show full stderr[17:26:01] This is snippy 4.6.0 [17:26:01] Written by Torsten Seemann [17:26:01] Obtained from https://github.com/tseemann/snippy [17:26:01] Detected operating system: linux [17:26:01] Enabling bundled linux tools. [17:26:01] Found bwa - /usr/local/bin/bwa [17:26:01] Found bcftools - /usr/local/bin/bcftools [17:26:01] Found samtools - /usr/local/bin/samtools [17:26:01] Found java - /usr/local/bin/java [17:26:01] Found snpEff - /usr/local/bin/snpEff [17:26:01] Found samclip - /usr/local/bin/samclip [17:26:01] Found seqtk - /usr/local/bin/seqtk [17:26:01] Found parallel - /usr/local/bin/parallel [17:26:01] Found freebayes - /usr/local/bin/freebayes [17:26:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:26:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:26:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:26:01] Found vcfuniq - /usr/local/bin/vcfuniq [17:26:01] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:26:01] Found gzip - /bin/gzip [17:26:01] Found vt - /usr/local/bin/vt [17:26:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:26:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:26:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:26:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:26:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:26:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:26:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:26:02] Please supply a reference FASTA/GBK/EMBL file with --reference
1[18:01:17] This is snippy 4.6.0
Show full stderr[18:01:17] This is snippy 4.6.0 [18:01:17] Written by Torsten Seemann [18:01:17] Obtained from https://github.com/tseemann/snippy [18:01:17] Detected operating system: linux [18:01:17] Enabling bundled linux tools. [18:01:17] Found bwa - /usr/local/bin/bwa [18:01:17] Found bcftools - /usr/local/bin/bcftools [18:01:17] Found samtools - /usr/local/bin/samtools [18:01:17] Found java - /usr/local/bin/java [18:01:17] Found snpEff - /usr/local/bin/snpEff [18:01:17] Found samclip - /usr/local/bin/samclip [18:01:17] Found seqtk - /usr/local/bin/seqtk [18:01:17] Found parallel - /usr/local/bin/parallel [18:01:17] Found freebayes - /usr/local/bin/freebayes [18:01:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [18:01:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [18:01:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [18:01:17] Found vcfuniq - /usr/local/bin/vcfuniq [18:01:17] Found vcffirstheader - /usr/local/bin/vcffirstheader [18:01:17] Found gzip - /bin/gzip [18:01:17] Found vt - /usr/local/bin/vt [18:01:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [18:01:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [18:01:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [18:01:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [18:01:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [18:01:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [18:01:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [18:01:18] Please supply a reference FASTA/GBK/EMBL file with --reference
1[18:26:27] This is snippy 4.6.0
Show full stderr[18:26:27] This is snippy 4.6.0 [18:26:27] Written by Torsten Seemann [18:26:27] Obtained from https://github.com/tseemann/snippy [18:26:27] Detected operating system: linux [18:26:27] Enabling bundled linux tools. [18:26:27] Found bwa - /usr/local/bin/bwa [18:26:27] Found bcftools - /usr/local/bin/bcftools [18:26:27] Found samtools - /usr/local/bin/samtools [18:26:27] Found java - /usr/local/bin/java [18:26:27] Found snpEff - /usr/local/bin/snpEff [18:26:27] Found samclip - /usr/local/bin/samclip [18:26:27] Found seqtk - /usr/local/bin/seqtk [18:26:27] Found parallel - /usr/local/bin/parallel [18:26:27] Found freebayes - /usr/local/bin/freebayes [18:26:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [18:26:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [18:26:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [18:26:27] Found vcfuniq - /usr/local/bin/vcfuniq [18:26:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [18:26:27] Found gzip - /bin/gzip [18:26:27] Found vt - /usr/local/bin/vt [18:26:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [18:26:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [18:26:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [18:26:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [18:26:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [18:26:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [18:26:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [18:26:28] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:16:59] This is snippy 4.6.0
Show full stderr[17:16:59] This is snippy 4.6.0 [17:16:59] Written by Torsten Seemann [17:16:59] Obtained from https://github.com/tseemann/snippy [17:16:59] Detected operating system: linux [17:16:59] Enabling bundled linux tools. [17:16:59] Found bwa - /usr/local/bin/bwa [17:16:59] Found bcftools - /usr/local/bin/bcftools [17:16:59] Found samtools - /usr/local/bin/samtools [17:16:59] Found java - /usr/local/bin/java [17:16:59] Found snpEff - /usr/local/bin/snpEff [17:16:59] Found samclip - /usr/local/bin/samclip [17:16:59] Found seqtk - /usr/local/bin/seqtk [17:16:59] Found parallel - /usr/local/bin/parallel [17:16:59] Found freebayes - /usr/local/bin/freebayes [17:16:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:16:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:16:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:16:59] Found vcfuniq - /usr/local/bin/vcfuniq [17:16:59] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:16:59] Found gzip - /bin/gzip [17:16:59] Found vt - /usr/local/bin/vt [17:16:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:16:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:16:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:16:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:16:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:17:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:17:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:17:00] Please supply a reference FASTA/GBK/EMBL file with --reference
1[18:43:18] This is snippy 4.6.0
Show full stderr[18:43:18] This is snippy 4.6.0 [18:43:18] Written by Torsten Seemann [18:43:18] Obtained from https://github.com/tseemann/snippy [18:43:18] Detected operating system: linux [18:43:18] Enabling bundled linux tools. [18:43:18] Found bwa - /usr/local/bin/bwa [18:43:18] Found bcftools - /usr/local/bin/bcftools [18:43:18] Found samtools - /usr/local/bin/samtools [18:43:18] Found java - /usr/local/bin/java [18:43:18] Found snpEff - /usr/local/bin/snpEff [18:43:18] Found samclip - /usr/local/bin/samclip [18:43:18] Found seqtk - /usr/local/bin/seqtk [18:43:18] Found parallel - /usr/local/bin/parallel [18:43:18] Found freebayes - /usr/local/bin/freebayes [18:43:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [18:43:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [18:43:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [18:43:18] Found vcfuniq - /usr/local/bin/vcfuniq [18:43:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [18:43:18] Found gzip - /bin/gzip [18:43:18] Found vt - /usr/local/bin/vt [18:43:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [18:43:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [18:43:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [18:43:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [18:43:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [18:43:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [18:43:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [18:43:19] Please supply a reference FASTA/GBK/EMBL file with --reference
1[18:59:04] This is snippy 4.6.0
Show full stderr[18:59:04] This is snippy 4.6.0 [18:59:04] Written by Torsten Seemann [18:59:04] Obtained from https://github.com/tseemann/snippy [18:59:04] Detected operating system: linux [18:59:04] Enabling bundled linux tools. [18:59:04] Found bwa - /usr/local/bin/bwa [18:59:04] Found bcftools - /usr/local/bin/bcftools [18:59:04] Found samtools - /usr/local/bin/samtools [18:59:04] Found java - /usr/local/bin/java [18:59:04] Found snpEff - /usr/local/bin/snpEff [18:59:04] Found samclip - /usr/local/bin/samclip [18:59:04] Found seqtk - /usr/local/bin/seqtk [18:59:04] Found parallel - /usr/local/bin/parallel [18:59:04] Found freebayes - /usr/local/bin/freebayes [18:59:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [18:59:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [18:59:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [18:59:04] Found vcfuniq - /usr/local/bin/vcfuniq [18:59:04] Found vcffirstheader - /usr/local/bin/vcffirstheader [18:59:04] Found gzip - /bin/gzip [18:59:04] Found vt - /usr/local/bin/vt [18:59:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [18:59:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [18:59:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [18:59:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [18:59:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [18:59:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [18:59:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [18:59:05] Please supply a reference FASTA/GBK/EMBL file with --reference
1[18:59:19] This is snippy 4.6.0
Show full stderr[18:59:19] This is snippy 4.6.0 [18:59:19] Written by Torsten Seemann [18:59:19] Obtained from https://github.com/tseemann/snippy [18:59:19] Detected operating system: linux [18:59:19] Enabling bundled linux tools. [18:59:19] Found bwa - /usr/local/bin/bwa [18:59:19] Found bcftools - /usr/local/bin/bcftools [18:59:19] Found samtools - /usr/local/bin/samtools [18:59:19] Found java - /usr/local/bin/java [18:59:19] Found snpEff - /usr/local/bin/snpEff [18:59:19] Found samclip - /usr/local/bin/samclip [18:59:19] Found seqtk - /usr/local/bin/seqtk [18:59:19] Found parallel - /usr/local/bin/parallel [18:59:19] Found freebayes - /usr/local/bin/freebayes [18:59:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [18:59:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [18:59:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [18:59:19] Found vcfuniq - /usr/local/bin/vcfuniq [18:59:19] Found vcffirstheader - /usr/local/bin/vcffirstheader [18:59:19] Found gzip - /bin/gzip [18:59:19] Found vt - /usr/local/bin/vt [18:59:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [18:59:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [18:59:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [18:59:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [18:59:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [18:59:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [18:59:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [18:59:20] Please supply a reference FASTA/GBK/EMBL file with --reference
1[19:07:46] This is snippy 4.6.0
Show full stderr[19:07:46] This is snippy 4.6.0 [19:07:46] Written by Torsten Seemann [19:07:46] Obtained from https://github.com/tseemann/snippy [19:07:46] Detected operating system: linux [19:07:46] Enabling bundled linux tools. [19:07:46] Found bwa - /usr/local/bin/bwa [19:07:46] Found bcftools - /usr/local/bin/bcftools [19:07:46] Found samtools - /usr/local/bin/samtools [19:07:46] Found java - /usr/local/bin/java [19:07:46] Found snpEff - /usr/local/bin/snpEff [19:07:46] Found samclip - /usr/local/bin/samclip [19:07:46] Found seqtk - /usr/local/bin/seqtk [19:07:46] Found parallel - /usr/local/bin/parallel [19:07:46] Found freebayes - /usr/local/bin/freebayes [19:07:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [19:07:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [19:07:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [19:07:46] Found vcfuniq - /usr/local/bin/vcfuniq [19:07:46] Found vcffirstheader - /usr/local/bin/vcffirstheader [19:07:46] Found gzip - /bin/gzip [19:07:46] Found vt - /usr/local/bin/vt [19:07:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [19:07:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [19:07:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [19:07:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [19:07:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [19:07:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [19:07:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [19:07:47] Please supply a reference FASTA/GBK/EMBL file with --reference
1[19:24:31] This is snippy 4.6.0
Show full stderr[19:24:31] This is snippy 4.6.0 [19:24:31] Written by Torsten Seemann [19:24:31] Obtained from https://github.com/tseemann/snippy [19:24:31] Detected operating system: linux [19:24:31] Enabling bundled linux tools. [19:24:31] Found bwa - /usr/local/bin/bwa [19:24:31] Found bcftools - /usr/local/bin/bcftools [19:24:31] Found samtools - /usr/local/bin/samtools [19:24:31] Found java - /usr/local/bin/java [19:24:31] Found snpEff - /usr/local/bin/snpEff [19:24:31] Found samclip - /usr/local/bin/samclip [19:24:32] Found seqtk - /usr/local/bin/seqtk [19:24:32] Found parallel - /usr/local/bin/parallel [19:24:32] Found freebayes - /usr/local/bin/freebayes [19:24:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [19:24:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [19:24:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [19:24:32] Found vcfuniq - /usr/local/bin/vcfuniq [19:24:32] Found vcffirstheader - /usr/local/bin/vcffirstheader [19:24:32] Found gzip - /bin/gzip [19:24:32] Found vt - /usr/local/bin/vt [19:24:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [19:24:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [19:24:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [19:24:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [19:24:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [19:24:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [19:24:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [19:24:32] Please supply a reference FASTA/GBK/EMBL file with --reference
1[19:48:57] This is snippy 4.6.0
Show full stderr[19:48:57] This is snippy 4.6.0 [19:48:57] Written by Torsten Seemann [19:48:57] Obtained from https://github.com/tseemann/snippy [19:48:57] Detected operating system: linux [19:48:57] Enabling bundled linux tools. [19:48:57] Found bwa - /usr/local/bin/bwa [19:48:57] Found bcftools - /usr/local/bin/bcftools [19:48:57] Found samtools - /usr/local/bin/samtools [19:48:57] Found java - /usr/local/bin/java [19:48:57] Found snpEff - /usr/local/bin/snpEff [19:48:57] Found samclip - /usr/local/bin/samclip [19:48:57] Found seqtk - /usr/local/bin/seqtk [19:48:57] Found parallel - /usr/local/bin/parallel [19:48:57] Found freebayes - /usr/local/bin/freebayes [19:48:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [19:48:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [19:48:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [19:48:57] Found vcfuniq - /usr/local/bin/vcfuniq [19:48:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [19:48:57] Found gzip - /bin/gzip [19:48:57] Found vt - /usr/local/bin/vt [19:48:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [19:48:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [19:48:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [19:48:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [19:48:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [19:48:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [19:48:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [19:48:58] Please supply a reference FASTA/GBK/EMBL file with --reference
1[18:18:12] This is snippy 4.6.0
Show full stderr[18:18:12] This is snippy 4.6.0 [18:18:12] Written by Torsten Seemann [18:18:12] Obtained from https://github.com/tseemann/snippy [18:18:12] Detected operating system: linux [18:18:12] Enabling bundled linux tools. [18:18:13] Found bwa - /usr/local/bin/bwa [18:18:13] Found bcftools - /usr/local/bin/bcftools [18:18:13] Found samtools - /usr/local/bin/samtools [18:18:13] Found java - /usr/local/bin/java [18:18:13] Found snpEff - /usr/local/bin/snpEff [18:18:13] Found samclip - /usr/local/bin/samclip [18:18:13] Found seqtk - /usr/local/bin/seqtk [18:18:13] Found parallel - /usr/local/bin/parallel [18:18:13] Found freebayes - /usr/local/bin/freebayes [18:18:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [18:18:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [18:18:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [18:18:13] Found vcfuniq - /usr/local/bin/vcfuniq [18:18:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [18:18:13] Found gzip - /bin/gzip [18:18:13] Found vt - /usr/local/bin/vt [18:18:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [18:18:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [18:18:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [18:18:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [18:18:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [18:18:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [18:18:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [18:18:13] Please supply a reference FASTA/GBK/EMBL file with --reference
1[18:26:44] This is snippy 4.6.0
Show full stderr[18:26:44] This is snippy 4.6.0 [18:26:44] Written by Torsten Seemann [18:26:44] Obtained from https://github.com/tseemann/snippy [18:26:44] Detected operating system: linux [18:26:44] Enabling bundled linux tools. [18:26:44] Found bwa - /usr/local/bin/bwa [18:26:44] Found bcftools - /usr/local/bin/bcftools [18:26:44] Found samtools - /usr/local/bin/samtools [18:26:44] Found java - /usr/local/bin/java [18:26:44] Found snpEff - /usr/local/bin/snpEff [18:26:44] Found samclip - /usr/local/bin/samclip [18:26:44] Found seqtk - /usr/local/bin/seqtk [18:26:44] Found parallel - /usr/local/bin/parallel [18:26:44] Found freebayes - /usr/local/bin/freebayes [18:26:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [18:26:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [18:26:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [18:26:44] Found vcfuniq - /usr/local/bin/vcfuniq [18:26:44] Found vcffirstheader - /usr/local/bin/vcffirstheader [18:26:44] Found gzip - /bin/gzip [18:26:44] Found vt - /usr/local/bin/vt [18:26:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [18:26:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [18:26:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [18:26:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [18:26:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [18:26:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [18:26:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [18:26:45] Please supply a reference FASTA/GBK/EMBL file with --reference
1[18:27:18] This is snippy 4.6.0
Show full stderr[18:27:18] This is snippy 4.6.0 [18:27:18] Written by Torsten Seemann [18:27:18] Obtained from https://github.com/tseemann/snippy [18:27:18] Detected operating system: linux [18:27:18] Enabling bundled linux tools. [18:27:18] Found bwa - /usr/local/bin/bwa [18:27:18] Found bcftools - /usr/local/bin/bcftools [18:27:19] Found samtools - /usr/local/bin/samtools [18:27:19] Found java - /usr/local/bin/java [18:27:19] Found snpEff - /usr/local/bin/snpEff [18:27:19] Found samclip - /usr/local/bin/samclip [18:27:19] Found seqtk - /usr/local/bin/seqtk [18:27:19] Found parallel - /usr/local/bin/parallel [18:27:19] Found freebayes - /usr/local/bin/freebayes [18:27:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [18:27:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [18:27:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [18:27:19] Found vcfuniq - /usr/local/bin/vcfuniq [18:27:19] Found vcffirstheader - /usr/local/bin/vcffirstheader [18:27:19] Found gzip - /bin/gzip [18:27:19] Found vt - /usr/local/bin/vt [18:27:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [18:27:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [18:27:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [18:27:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [18:27:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [18:27:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [18:27:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [18:27:21] Please supply a reference FASTA/GBK/EMBL file with --reference
1[18:35:18] This is snippy 4.6.0
Show full stderr[18:35:18] This is snippy 4.6.0 [18:35:18] Written by Torsten Seemann [18:35:18] Obtained from https://github.com/tseemann/snippy [18:35:18] Detected operating system: linux [18:35:18] Enabling bundled linux tools. [18:35:18] Found bwa - /usr/local/bin/bwa [18:35:18] Found bcftools - /usr/local/bin/bcftools [18:35:18] Found samtools - /usr/local/bin/samtools [18:35:18] Found java - /usr/local/bin/java [18:35:18] Found snpEff - /usr/local/bin/snpEff [18:35:18] Found samclip - /usr/local/bin/samclip [18:35:18] Found seqtk - /usr/local/bin/seqtk [18:35:18] Found parallel - /usr/local/bin/parallel [18:35:18] Found freebayes - /usr/local/bin/freebayes [18:35:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [18:35:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [18:35:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [18:35:18] Found vcfuniq - /usr/local/bin/vcfuniq [18:35:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [18:35:18] Found gzip - /bin/gzip [18:35:18] Found vt - /usr/local/bin/vt [18:35:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [18:35:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [18:35:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [18:35:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [18:35:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [18:35:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [18:35:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [18:35:18] Please supply a reference FASTA/GBK/EMBL file with --reference
1[18:59:48] This is snippy 4.6.0
Show full stderr[18:59:48] This is snippy 4.6.0 [18:59:48] Written by Torsten Seemann [18:59:48] Obtained from https://github.com/tseemann/snippy [18:59:48] Detected operating system: linux [18:59:48] Enabling bundled linux tools. [18:59:48] Found bwa - /usr/local/bin/bwa [18:59:48] Found bcftools - /usr/local/bin/bcftools [18:59:48] Found samtools - /usr/local/bin/samtools [18:59:48] Found java - /usr/local/bin/java [18:59:48] Found snpEff - /usr/local/bin/snpEff [18:59:48] Found samclip - /usr/local/bin/samclip [18:59:48] Found seqtk - /usr/local/bin/seqtk [18:59:48] Found parallel - /usr/local/bin/parallel [18:59:48] Found freebayes - /usr/local/bin/freebayes [18:59:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [18:59:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [18:59:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [18:59:48] Found vcfuniq - /usr/local/bin/vcfuniq [18:59:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [18:59:48] Found gzip - /bin/gzip [18:59:48] Found vt - /usr/local/bin/vt [18:59:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [18:59:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [18:59:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [18:59:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [18:59:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [18:59:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [18:59:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [18:59:49] Please supply a reference FASTA/GBK/EMBL file with --reference
1[19:08:18] This is snippy 4.6.0
Show full stderr[19:08:18] This is snippy 4.6.0 [19:08:18] Written by Torsten Seemann [19:08:18] Obtained from https://github.com/tseemann/snippy [19:08:18] Detected operating system: linux [19:08:18] Enabling bundled linux tools. [19:08:18] Found bwa - /usr/local/bin/bwa [19:08:18] Found bcftools - /usr/local/bin/bcftools [19:08:18] Found samtools - /usr/local/bin/samtools [19:08:18] Found java - /usr/local/bin/java [19:08:18] Found snpEff - /usr/local/bin/snpEff [19:08:18] Found samclip - /usr/local/bin/samclip [19:08:18] Found seqtk - /usr/local/bin/seqtk [19:08:18] Found parallel - /usr/local/bin/parallel [19:08:18] Found freebayes - /usr/local/bin/freebayes [19:08:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [19:08:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [19:08:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [19:08:18] Found vcfuniq - /usr/local/bin/vcfuniq [19:08:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [19:08:18] Found gzip - /bin/gzip [19:08:18] Found vt - /usr/local/bin/vt [19:08:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [19:08:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [19:08:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [19:08:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [19:08:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [19:08:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [19:08:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [19:08:18] Please supply a reference FASTA/GBK/EMBL file with --reference
1[19:16:18] This is snippy 4.6.0
Show full stderr[19:16:18] This is snippy 4.6.0 [19:16:18] Written by Torsten Seemann [19:16:18] Obtained from https://github.com/tseemann/snippy [19:16:18] Detected operating system: linux [19:16:18] Enabling bundled linux tools. [19:16:18] Found bwa - /usr/local/bin/bwa [19:16:18] Found bcftools - /usr/local/bin/bcftools [19:16:18] Found samtools - /usr/local/bin/samtools [19:16:18] Found java - /usr/local/bin/java [19:16:18] Found snpEff - /usr/local/bin/snpEff [19:16:18] Found samclip - /usr/local/bin/samclip [19:16:18] Found seqtk - /usr/local/bin/seqtk [19:16:18] Found parallel - /usr/local/bin/parallel [19:16:18] Found freebayes - /usr/local/bin/freebayes [19:16:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [19:16:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [19:16:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [19:16:18] Found vcfuniq - /usr/local/bin/vcfuniq [19:16:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [19:16:18] Found gzip - /bin/gzip [19:16:18] Found vt - /usr/local/bin/vt [19:16:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [19:16:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [19:16:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [19:16:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [19:16:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [19:16:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [19:16:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [19:16:19] Please supply a reference FASTA/GBK/EMBL file with --reference
1[19:25:18] This is snippy 4.6.0
Show full stderr[19:25:18] This is snippy 4.6.0 [19:25:18] Written by Torsten Seemann [19:25:18] Obtained from https://github.com/tseemann/snippy [19:25:18] Detected operating system: linux [19:25:18] Enabling bundled linux tools. [19:25:18] Found bwa - /usr/local/bin/bwa [19:25:18] Found bcftools - /usr/local/bin/bcftools [19:25:18] Found samtools - /usr/local/bin/samtools [19:25:18] Found java - /usr/local/bin/java [19:25:18] Found snpEff - /usr/local/bin/snpEff [19:25:18] Found samclip - /usr/local/bin/samclip [19:25:18] Found seqtk - /usr/local/bin/seqtk [19:25:18] Found parallel - /usr/local/bin/parallel [19:25:18] Found freebayes - /usr/local/bin/freebayes [19:25:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [19:25:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [19:25:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [19:25:18] Found vcfuniq - /usr/local/bin/vcfuniq [19:25:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [19:25:18] Found gzip - /bin/gzip [19:25:18] Found vt - /usr/local/bin/vt [19:25:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [19:25:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [19:25:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [19:25:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [19:25:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [19:25:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [19:25:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [19:25:19] Please supply a reference FASTA/GBK/EMBL file with --reference
1[19:40:57] This is snippy 4.6.0
Show full stderr[19:40:57] This is snippy 4.6.0 [19:40:57] Written by Torsten Seemann [19:40:57] Obtained from https://github.com/tseemann/snippy [19:40:57] Detected operating system: linux [19:40:57] Enabling bundled linux tools. [19:40:57] Found bwa - /usr/local/bin/bwa [19:40:57] Found bcftools - /usr/local/bin/bcftools [19:40:57] Found samtools - /usr/local/bin/samtools [19:40:58] Found java - /usr/local/bin/java [19:40:58] Found snpEff - /usr/local/bin/snpEff [19:40:58] Found samclip - /usr/local/bin/samclip [19:40:58] Found seqtk - /usr/local/bin/seqtk [19:40:58] Found parallel - /usr/local/bin/parallel [19:40:58] Found freebayes - /usr/local/bin/freebayes [19:40:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [19:40:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [19:40:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [19:40:58] Found vcfuniq - /usr/local/bin/vcfuniq [19:40:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [19:40:58] Found gzip - /bin/gzip [19:40:58] Found vt - /usr/local/bin/vt [19:40:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [19:40:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [19:40:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [19:40:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [19:40:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [19:40:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [19:40:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [19:40:58] Please supply a reference FASTA/GBK/EMBL file with --reference
1[19:41:18] This is snippy 4.6.0
Show full stderr[19:41:18] This is snippy 4.6.0 [19:41:18] Written by Torsten Seemann [19:41:18] Obtained from https://github.com/tseemann/snippy [19:41:18] Detected operating system: linux [19:41:18] Enabling bundled linux tools. [19:41:18] Found bwa - /usr/local/bin/bwa [19:41:18] Found bcftools - /usr/local/bin/bcftools [19:41:18] Found samtools - /usr/local/bin/samtools [19:41:18] Found java - /usr/local/bin/java [19:41:18] Found snpEff - /usr/local/bin/snpEff [19:41:18] Found samclip - /usr/local/bin/samclip [19:41:18] Found seqtk - /usr/local/bin/seqtk [19:41:18] Found parallel - /usr/local/bin/parallel [19:41:18] Found freebayes - /usr/local/bin/freebayes [19:41:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [19:41:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [19:41:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [19:41:18] Found vcfuniq - /usr/local/bin/vcfuniq [19:41:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [19:41:18] Found gzip - /bin/gzip [19:41:18] Found vt - /usr/local/bin/vt [19:41:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [19:41:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [19:41:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [19:41:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [19:41:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [19:41:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [19:41:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [19:41:18] Please supply a reference FASTA/GBK/EMBL file with --reference
1[19:48:58] This is snippy 4.6.0
Show full stderr[19:48:58] This is snippy 4.6.0 [19:48:58] Written by Torsten Seemann [19:48:58] Obtained from https://github.com/tseemann/snippy [19:48:58] Detected operating system: linux [19:48:58] Enabling bundled linux tools. [19:48:58] Found bwa - /usr/local/bin/bwa [19:48:58] Found bcftools - /usr/local/bin/bcftools [19:48:58] Found samtools - /usr/local/bin/samtools [19:48:58] Found java - /usr/local/bin/java [19:48:58] Found snpEff - /usr/local/bin/snpEff [19:48:58] Found samclip - /usr/local/bin/samclip [19:48:58] Found seqtk - /usr/local/bin/seqtk [19:48:58] Found parallel - /usr/local/bin/parallel [19:48:58] Found freebayes - /usr/local/bin/freebayes [19:48:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [19:48:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [19:48:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [19:48:58] Found vcfuniq - /usr/local/bin/vcfuniq [19:48:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [19:48:58] Found gzip - /bin/gzip [19:48:58] Found vt - /usr/local/bin/vt [19:48:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [19:48:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [19:48:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [19:48:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [19:48:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [19:48:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [19:48:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [19:48:59] Please supply a reference FASTA/GBK/EMBL file with --reference
1[20:13:46] This is snippy 4.6.0
Show full stderr[20:13:46] This is snippy 4.6.0 [20:13:46] Written by Torsten Seemann [20:13:46] Obtained from https://github.com/tseemann/snippy [20:13:46] Detected operating system: linux [20:13:46] Enabling bundled linux tools. [20:13:46] Found bwa - /usr/local/bin/bwa [20:13:46] Found bcftools - /usr/local/bin/bcftools [20:13:46] Found samtools - /usr/local/bin/samtools [20:13:46] Found java - /usr/local/bin/java [20:13:46] Found snpEff - /usr/local/bin/snpEff [20:13:46] Found samclip - /usr/local/bin/samclip [20:13:46] Found seqtk - /usr/local/bin/seqtk [20:13:46] Found parallel - /usr/local/bin/parallel [20:13:46] Found freebayes - /usr/local/bin/freebayes [20:13:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [20:13:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [20:13:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [20:13:46] Found vcfuniq - /usr/local/bin/vcfuniq [20:13:46] Found vcffirstheader - /usr/local/bin/vcffirstheader [20:13:46] Found gzip - /bin/gzip [20:13:46] Found vt - /usr/local/bin/vt [20:13:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [20:13:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [20:13:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [20:13:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [20:13:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [20:13:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [20:13:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [20:13:47] Please supply a reference FASTA/GBK/EMBL file with --reference
1[20:14:15] This is snippy 4.6.0
Show full stderr[20:14:15] This is snippy 4.6.0 [20:14:15] Written by Torsten Seemann [20:14:15] Obtained from https://github.com/tseemann/snippy [20:14:15] Detected operating system: linux [20:14:15] Enabling bundled linux tools. [20:14:15] Found bwa - /usr/local/bin/bwa [20:14:15] Found bcftools - /usr/local/bin/bcftools [20:14:15] Found samtools - /usr/local/bin/samtools [20:14:15] Found java - /usr/local/bin/java [20:14:15] Found snpEff - /usr/local/bin/snpEff [20:14:15] Found samclip - /usr/local/bin/samclip [20:14:15] Found seqtk - /usr/local/bin/seqtk [20:14:15] Found parallel - /usr/local/bin/parallel [20:14:15] Found freebayes - /usr/local/bin/freebayes [20:14:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [20:14:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [20:14:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [20:14:15] Found vcfuniq - /usr/local/bin/vcfuniq [20:14:15] Found vcffirstheader - /usr/local/bin/vcffirstheader [20:14:15] Found gzip - /bin/gzip [20:14:15] Found vt - /usr/local/bin/vt [20:14:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [20:14:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [20:14:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [20:14:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [20:14:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [20:14:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [20:14:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [20:14:16] Please supply a reference FASTA/GBK/EMBL file with --reference
1[15:56:26] This is snippy 4.6.0
Show full stderr[15:56:26] This is snippy 4.6.0 [15:56:26] Written by Torsten Seemann [15:56:26] Obtained from https://github.com/tseemann/snippy [15:56:26] Detected operating system: linux [15:56:26] Enabling bundled linux tools. [15:56:26] Found bwa - /usr/local/bin/bwa [15:56:26] Found bcftools - /usr/local/bin/bcftools [15:56:26] Found samtools - /usr/local/bin/samtools [15:56:26] Found java - /usr/local/bin/java [15:56:26] Found snpEff - /usr/local/bin/snpEff [15:56:26] Found samclip - /usr/local/bin/samclip [15:56:26] Found seqtk - /usr/local/bin/seqtk [15:56:26] Found parallel - /usr/local/bin/parallel [15:56:26] Found freebayes - /usr/local/bin/freebayes [15:56:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [15:56:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [15:56:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [15:56:26] Found vcfuniq - /usr/local/bin/vcfuniq [15:56:26] Found vcffirstheader - /usr/local/bin/vcffirstheader [15:56:26] Found gzip - /bin/gzip [15:56:26] Found vt - /usr/local/bin/vt [15:56:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [15:56:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [15:56:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [15:56:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [15:56:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [15:56:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [15:56:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [15:56:27] Please supply a reference FASTA/GBK/EMBL file with --reference
1[20:22:49] This is snippy 4.6.0
Show full stderr[20:22:49] This is snippy 4.6.0 [20:22:49] Written by Torsten Seemann [20:22:49] Obtained from https://github.com/tseemann/snippy [20:22:49] Detected operating system: linux [20:22:49] Enabling bundled linux tools. [20:22:49] Found bwa - /usr/local/bin/bwa [20:22:49] Found bcftools - /usr/local/bin/bcftools [20:22:49] Found samtools - /usr/local/bin/samtools [20:22:49] Found java - /usr/local/bin/java [20:22:49] Found snpEff - /usr/local/bin/snpEff [20:22:49] Found samclip - /usr/local/bin/samclip [20:22:49] Found seqtk - /usr/local/bin/seqtk [20:22:49] Found parallel - /usr/local/bin/parallel [20:22:49] Found freebayes - /usr/local/bin/freebayes [20:22:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [20:22:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [20:22:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [20:22:49] Found vcfuniq - /usr/local/bin/vcfuniq [20:22:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [20:22:49] Found gzip - /bin/gzip [20:22:49] Found vt - /usr/local/bin/vt [20:22:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [20:22:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [20:22:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [20:22:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [20:22:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [20:22:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [20:22:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [20:22:51] Please supply a reference FASTA/GBK/EMBL file with --reference
1[20:05:48] This is snippy 4.6.0
Show full stderr[20:05:48] This is snippy 4.6.0 [20:05:48] Written by Torsten Seemann [20:05:48] Obtained from https://github.com/tseemann/snippy [20:05:48] Detected operating system: linux [20:05:48] Enabling bundled linux tools. [20:05:48] Found bwa - /usr/local/bin/bwa [20:05:48] Found bcftools - /usr/local/bin/bcftools [20:05:48] Found samtools - /usr/local/bin/samtools [20:05:48] Found java - /usr/local/bin/java [20:05:48] Found snpEff - /usr/local/bin/snpEff [20:05:48] Found samclip - /usr/local/bin/samclip [20:05:48] Found seqtk - /usr/local/bin/seqtk [20:05:48] Found parallel - /usr/local/bin/parallel [20:05:48] Found freebayes - /usr/local/bin/freebayes [20:05:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [20:05:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [20:05:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [20:05:48] Found vcfuniq - /usr/local/bin/vcfuniq [20:05:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [20:05:48] Found gzip - /bin/gzip [20:05:48] Found vt - /usr/local/bin/vt [20:05:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [20:05:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [20:05:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [20:05:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [20:05:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [20:05:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [20:05:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [20:05:49] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:45:17] This is snippy 4.6.0
Show full stderr[00:45:17] This is snippy 4.6.0 [00:45:17] Written by Torsten Seemann [00:45:17] Obtained from https://github.com/tseemann/snippy [00:45:17] Detected operating system: linux [00:45:17] Enabling bundled linux tools. [00:45:17] Found bwa - /usr/local/bin/bwa [00:45:17] Found bcftools - /usr/local/bin/bcftools [00:45:17] Found samtools - /usr/local/bin/samtools [00:45:17] Found java - /usr/local/bin/java [00:45:17] Found snpEff - /usr/local/bin/snpEff [00:45:17] Found samclip - /usr/local/bin/samclip [00:45:17] Found seqtk - /usr/local/bin/seqtk [00:45:17] Found parallel - /usr/local/bin/parallel [00:45:17] Found freebayes - /usr/local/bin/freebayes [00:45:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:45:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:45:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:45:17] Found vcfuniq - /usr/local/bin/vcfuniq [00:45:17] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:45:17] Found gzip - /bin/gzip [00:45:17] Found vt - /usr/local/bin/vt [00:45:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:45:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:45:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:45:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:45:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:45:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:45:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:45:18] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:01:17] This is snippy 4.6.0
Show full stderr[01:01:17] This is snippy 4.6.0 [01:01:17] Written by Torsten Seemann [01:01:17] Obtained from https://github.com/tseemann/snippy [01:01:17] Detected operating system: linux [01:01:17] Enabling bundled linux tools. [01:01:17] Found bwa - /usr/local/bin/bwa [01:01:17] Found bcftools - /usr/local/bin/bcftools [01:01:17] Found samtools - /usr/local/bin/samtools [01:01:17] Found java - /usr/local/bin/java [01:01:17] Found snpEff - /usr/local/bin/snpEff [01:01:17] Found samclip - /usr/local/bin/samclip [01:01:17] Found seqtk - /usr/local/bin/seqtk [01:01:17] Found parallel - /usr/local/bin/parallel [01:01:17] Found freebayes - /usr/local/bin/freebayes [01:01:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:01:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:01:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:01:17] Found vcfuniq - /usr/local/bin/vcfuniq [01:01:17] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:01:17] Found gzip - /bin/gzip [01:01:17] Found vt - /usr/local/bin/vt [01:01:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:01:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:01:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:01:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:01:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:01:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:01:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:01:18] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:17:40] This is snippy 4.6.0
Show full stderr[01:17:40] This is snippy 4.6.0 [01:17:40] Written by Torsten Seemann [01:17:40] Obtained from https://github.com/tseemann/snippy [01:17:40] Detected operating system: linux [01:17:40] Enabling bundled linux tools. [01:17:40] Found bwa - /usr/local/bin/bwa [01:17:40] Found bcftools - /usr/local/bin/bcftools [01:17:40] Found samtools - /usr/local/bin/samtools [01:17:40] Found java - /usr/local/bin/java [01:17:40] Found snpEff - /usr/local/bin/snpEff [01:17:40] Found samclip - /usr/local/bin/samclip [01:17:40] Found seqtk - /usr/local/bin/seqtk [01:17:40] Found parallel - /usr/local/bin/parallel [01:17:40] Found freebayes - /usr/local/bin/freebayes [01:17:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:17:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:17:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:17:40] Found vcfuniq - /usr/local/bin/vcfuniq [01:17:40] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:17:40] Found gzip - /bin/gzip [01:17:40] Found vt - /usr/local/bin/vt [01:17:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:17:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:17:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:17:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:17:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:17:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:17:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:17:41] Please supply a reference FASTA/GBK/EMBL file with --reference
1[20:14:30] This is snippy 4.6.0
Show full stderr[20:14:30] This is snippy 4.6.0 [20:14:30] Written by Torsten Seemann [20:14:30] Obtained from https://github.com/tseemann/snippy [20:14:30] Detected operating system: linux [20:14:30] Enabling bundled linux tools. [20:14:30] Found bwa - /usr/local/bin/bwa [20:14:30] Found bcftools - /usr/local/bin/bcftools [20:14:30] Found samtools - /usr/local/bin/samtools [20:14:30] Found java - /usr/local/bin/java [20:14:30] Found snpEff - /usr/local/bin/snpEff [20:14:30] Found samclip - /usr/local/bin/samclip [20:14:30] Found seqtk - /usr/local/bin/seqtk [20:14:30] Found parallel - /usr/local/bin/parallel [20:14:30] Found freebayes - /usr/local/bin/freebayes [20:14:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [20:14:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [20:14:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [20:14:30] Found vcfuniq - /usr/local/bin/vcfuniq [20:14:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [20:14:30] Found gzip - /bin/gzip [20:14:30] Found vt - /usr/local/bin/vt [20:14:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [20:14:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [20:14:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [20:14:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [20:14:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [20:14:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [20:14:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [20:14:31] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:26:47] This is snippy 4.6.0
Show full stderr[01:26:47] This is snippy 4.6.0 [01:26:47] Written by Torsten Seemann [01:26:47] Obtained from https://github.com/tseemann/snippy [01:26:47] Detected operating system: linux [01:26:47] Enabling bundled linux tools. [01:26:47] Found bwa - /usr/local/bin/bwa [01:26:47] Found bcftools - /usr/local/bin/bcftools [01:26:47] Found samtools - /usr/local/bin/samtools [01:26:47] Found java - /usr/local/bin/java [01:26:47] Found snpEff - /usr/local/bin/snpEff [01:26:47] Found samclip - /usr/local/bin/samclip [01:26:47] Found seqtk - /usr/local/bin/seqtk [01:26:47] Found parallel - /usr/local/bin/parallel [01:26:47] Found freebayes - /usr/local/bin/freebayes [01:26:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:26:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:26:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:26:47] Found vcfuniq - /usr/local/bin/vcfuniq [01:26:47] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:26:47] Found gzip - /bin/gzip [01:26:47] Found vt - /usr/local/bin/vt [01:26:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:26:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:26:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:26:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:26:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:26:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:26:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:26:48] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:34:29] This is snippy 4.6.0
Show full stderr[01:34:29] This is snippy 4.6.0 [01:34:29] Written by Torsten Seemann [01:34:29] Obtained from https://github.com/tseemann/snippy [01:34:29] Detected operating system: linux [01:34:29] Enabling bundled linux tools. [01:34:29] Found bwa - /usr/local/bin/bwa [01:34:29] Found bcftools - /usr/local/bin/bcftools [01:34:29] Found samtools - /usr/local/bin/samtools [01:34:29] Found java - /usr/local/bin/java [01:34:29] Found snpEff - /usr/local/bin/snpEff [01:34:29] Found samclip - /usr/local/bin/samclip [01:34:29] Found seqtk - /usr/local/bin/seqtk [01:34:29] Found parallel - /usr/local/bin/parallel [01:34:29] Found freebayes - /usr/local/bin/freebayes [01:34:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:34:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:34:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:34:30] Found vcfuniq - /usr/local/bin/vcfuniq [01:34:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:34:30] Found gzip - /bin/gzip [01:34:30] Found vt - /usr/local/bin/vt [01:34:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:34:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:34:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:34:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:34:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:34:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:34:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:34:31] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:34:41] This is snippy 4.6.0
Show full stderr[01:34:41] This is snippy 4.6.0 [01:34:41] Written by Torsten Seemann [01:34:41] Obtained from https://github.com/tseemann/snippy [01:34:41] Detected operating system: linux [01:34:41] Enabling bundled linux tools. [01:34:41] Found bwa - /usr/local/bin/bwa [01:34:41] Found bcftools - /usr/local/bin/bcftools [01:34:41] Found samtools - /usr/local/bin/samtools [01:34:41] Found java - /usr/local/bin/java [01:34:41] Found snpEff - /usr/local/bin/snpEff [01:34:41] Found samclip - /usr/local/bin/samclip [01:34:41] Found seqtk - /usr/local/bin/seqtk [01:34:41] Found parallel - /usr/local/bin/parallel [01:34:41] Found freebayes - /usr/local/bin/freebayes [01:34:41] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:34:41] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:34:41] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:34:41] Found vcfuniq - /usr/local/bin/vcfuniq [01:34:41] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:34:41] Found gzip - /bin/gzip [01:34:41] Found vt - /usr/local/bin/vt [01:34:41] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:34:41] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:34:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:34:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:34:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:34:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:34:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:34:42] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:34:55] This is snippy 4.6.0
Show full stderr[01:34:55] This is snippy 4.6.0 [01:34:55] Written by Torsten Seemann [01:34:55] Obtained from https://github.com/tseemann/snippy [01:34:55] Detected operating system: linux [01:34:55] Enabling bundled linux tools. [01:34:55] Found bwa - /usr/local/bin/bwa [01:34:55] Found bcftools - /usr/local/bin/bcftools [01:34:55] Found samtools - /usr/local/bin/samtools [01:34:55] Found java - /usr/local/bin/java [01:34:55] Found snpEff - /usr/local/bin/snpEff [01:34:55] Found samclip - /usr/local/bin/samclip [01:34:55] Found seqtk - /usr/local/bin/seqtk [01:34:55] Found parallel - /usr/local/bin/parallel [01:34:55] Found freebayes - /usr/local/bin/freebayes [01:34:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:34:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:34:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:34:55] Found vcfuniq - /usr/local/bin/vcfuniq [01:34:55] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:34:55] Found gzip - /bin/gzip [01:34:55] Found vt - /usr/local/bin/vt [01:34:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:34:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:34:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:34:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:34:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:34:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:34:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:34:56] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:43:17] This is snippy 4.6.0
Show full stderr[01:43:17] This is snippy 4.6.0 [01:43:17] Written by Torsten Seemann [01:43:17] Obtained from https://github.com/tseemann/snippy [01:43:17] Detected operating system: linux [01:43:17] Enabling bundled linux tools. [01:43:17] Found bwa - /usr/local/bin/bwa [01:43:17] Found bcftools - /usr/local/bin/bcftools [01:43:17] Found samtools - /usr/local/bin/samtools [01:43:17] Found java - /usr/local/bin/java [01:43:17] Found snpEff - /usr/local/bin/snpEff [01:43:17] Found samclip - /usr/local/bin/samclip [01:43:17] Found seqtk - /usr/local/bin/seqtk [01:43:17] Found parallel - /usr/local/bin/parallel [01:43:17] Found freebayes - /usr/local/bin/freebayes [01:43:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:43:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:43:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:43:17] Found vcfuniq - /usr/local/bin/vcfuniq [01:43:17] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:43:17] Found gzip - /bin/gzip [01:43:17] Found vt - /usr/local/bin/vt [01:43:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:43:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:43:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:43:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:43:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:43:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:43:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:43:18] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:51:32] This is snippy 4.6.0
Show full stderr[01:51:32] This is snippy 4.6.0 [01:51:32] Written by Torsten Seemann [01:51:32] Obtained from https://github.com/tseemann/snippy [01:51:32] Detected operating system: linux [01:51:32] Enabling bundled linux tools. [01:51:32] Found bwa - /usr/local/bin/bwa [01:51:32] Found bcftools - /usr/local/bin/bcftools [01:51:32] Found samtools - /usr/local/bin/samtools [01:51:32] Found java - /usr/local/bin/java [01:51:32] Found snpEff - /usr/local/bin/snpEff [01:51:32] Found samclip - /usr/local/bin/samclip [01:51:32] Found seqtk - /usr/local/bin/seqtk [01:51:32] Found parallel - /usr/local/bin/parallel [01:51:32] Found freebayes - /usr/local/bin/freebayes [01:51:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:51:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:51:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:51:32] Found vcfuniq - /usr/local/bin/vcfuniq [01:51:32] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:51:32] Found gzip - /bin/gzip [01:51:32] Found vt - /usr/local/bin/vt [01:51:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:51:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:51:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:51:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:51:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:51:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:51:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:51:33] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:52:17] This is snippy 4.6.0
Show full stderr[01:52:17] This is snippy 4.6.0 [01:52:17] Written by Torsten Seemann [01:52:17] Obtained from https://github.com/tseemann/snippy [01:52:17] Detected operating system: linux [01:52:17] Enabling bundled linux tools. [01:52:17] Found bwa - /usr/local/bin/bwa [01:52:17] Found bcftools - /usr/local/bin/bcftools [01:52:17] Found samtools - /usr/local/bin/samtools [01:52:17] Found java - /usr/local/bin/java [01:52:17] Found snpEff - /usr/local/bin/snpEff [01:52:17] Found samclip - /usr/local/bin/samclip [01:52:17] Found seqtk - /usr/local/bin/seqtk [01:52:17] Found parallel - /usr/local/bin/parallel [01:52:17] Found freebayes - /usr/local/bin/freebayes [01:52:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:52:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:52:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:52:17] Found vcfuniq - /usr/local/bin/vcfuniq [01:52:17] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:52:17] Found gzip - /bin/gzip [01:52:17] Found vt - /usr/local/bin/vt [01:52:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:52:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:52:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:52:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:52:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:52:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:52:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:52:18] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:59:58] This is snippy 4.6.0
Show full stderr[01:59:58] This is snippy 4.6.0 [01:59:58] Written by Torsten Seemann [01:59:58] Obtained from https://github.com/tseemann/snippy [01:59:58] Detected operating system: linux [01:59:58] Enabling bundled linux tools. [01:59:58] Found bwa - /usr/local/bin/bwa [01:59:58] Found bcftools - /usr/local/bin/bcftools [01:59:58] Found samtools - /usr/local/bin/samtools [01:59:58] Found java - /usr/local/bin/java [01:59:58] Found snpEff - /usr/local/bin/snpEff [01:59:58] Found samclip - /usr/local/bin/samclip [01:59:58] Found seqtk - /usr/local/bin/seqtk [01:59:58] Found parallel - /usr/local/bin/parallel [01:59:58] Found freebayes - /usr/local/bin/freebayes [01:59:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:59:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:59:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:59:58] Found vcfuniq - /usr/local/bin/vcfuniq [01:59:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:59:58] Found gzip - /bin/gzip [01:59:58] Found vt - /usr/local/bin/vt [01:59:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:59:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:59:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:59:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:59:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:59:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:59:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:59:59] Please supply a reference FASTA/GBK/EMBL file with --reference
1[22:20:17] This is snippy 4.6.0
Show full stderr[22:20:17] This is snippy 4.6.0 [22:20:17] Written by Torsten Seemann [22:20:17] Obtained from https://github.com/tseemann/snippy [22:20:17] Detected operating system: linux [22:20:17] Enabling bundled linux tools. [22:20:17] Found bwa - /usr/local/bin/bwa [22:20:17] Found bcftools - /usr/local/bin/bcftools [22:20:17] Found samtools - /usr/local/bin/samtools [22:20:17] Found java - /usr/local/bin/java [22:20:17] Found snpEff - /usr/local/bin/snpEff [22:20:17] Found samclip - /usr/local/bin/samclip [22:20:17] Found seqtk - /usr/local/bin/seqtk [22:20:17] Found parallel - /usr/local/bin/parallel [22:20:17] Found freebayes - /usr/local/bin/freebayes [22:20:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [22:20:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [22:20:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [22:20:17] Found vcfuniq - /usr/local/bin/vcfuniq [22:20:17] Found vcffirstheader - /usr/local/bin/vcffirstheader [22:20:18] Found gzip - /bin/gzip [22:20:18] Found vt - /usr/local/bin/vt [22:20:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [22:20:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [22:20:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [22:20:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [22:20:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [22:20:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [22:20:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [22:20:18] Please supply a reference FASTA/GBK/EMBL file with --reference
1[22:29:17] This is snippy 4.6.0
Show full stderr[22:29:17] This is snippy 4.6.0 [22:29:17] Written by Torsten Seemann [22:29:17] Obtained from https://github.com/tseemann/snippy [22:29:17] Detected operating system: linux [22:29:17] Enabling bundled linux tools. [22:29:17] Found bwa - /usr/local/bin/bwa [22:29:17] Found bcftools - /usr/local/bin/bcftools [22:29:17] Found samtools - /usr/local/bin/samtools [22:29:17] Found java - /usr/local/bin/java [22:29:17] Found snpEff - /usr/local/bin/snpEff [22:29:17] Found samclip - /usr/local/bin/samclip [22:29:18] Found seqtk - /usr/local/bin/seqtk [22:29:18] Found parallel - /usr/local/bin/parallel [22:29:18] Found freebayes - /usr/local/bin/freebayes [22:29:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [22:29:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [22:29:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [22:29:18] Found vcfuniq - /usr/local/bin/vcfuniq [22:29:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [22:29:18] Found gzip - /bin/gzip [22:29:18] Found vt - /usr/local/bin/vt [22:29:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [22:29:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [22:29:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [22:29:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [22:29:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [22:29:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [22:29:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [22:29:18] Please supply a reference FASTA/GBK/EMBL file with --reference
1[23:01:52] This is snippy 4.6.0
Show full stderr[23:01:52] This is snippy 4.6.0 [23:01:52] Written by Torsten Seemann [23:01:52] Obtained from https://github.com/tseemann/snippy [23:01:52] Detected operating system: linux [23:01:52] Enabling bundled linux tools. [23:01:52] Found bwa - /usr/local/bin/bwa [23:01:52] Found bcftools - /usr/local/bin/bcftools [23:01:52] Found samtools - /usr/local/bin/samtools [23:01:52] Found java - /usr/local/bin/java [23:01:52] Found snpEff - /usr/local/bin/snpEff [23:01:52] Found samclip - /usr/local/bin/samclip [23:01:52] Found seqtk - /usr/local/bin/seqtk [23:01:52] Found parallel - /usr/local/bin/parallel [23:01:52] Found freebayes - /usr/local/bin/freebayes [23:01:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [23:01:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [23:01:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [23:01:52] Found vcfuniq - /usr/local/bin/vcfuniq [23:01:52] Found vcffirstheader - /usr/local/bin/vcffirstheader [23:01:52] Found gzip - /bin/gzip [23:01:52] Found vt - /usr/local/bin/vt [23:01:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [23:01:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [23:01:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [23:01:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [23:01:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [23:01:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [23:01:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [23:01:53] Please supply a reference FASTA/GBK/EMBL file with --reference
1[23:10:00] This is snippy 4.6.0
Show full stderr[23:10:00] This is snippy 4.6.0 [23:10:00] Written by Torsten Seemann [23:10:00] Obtained from https://github.com/tseemann/snippy [23:10:00] Detected operating system: linux [23:10:00] Enabling bundled linux tools. [23:10:00] Found bwa - /usr/local/bin/bwa [23:10:00] Found bcftools - /usr/local/bin/bcftools [23:10:00] Found samtools - /usr/local/bin/samtools [23:10:00] Found java - /usr/local/bin/java [23:10:00] Found snpEff - /usr/local/bin/snpEff [23:10:00] Found samclip - /usr/local/bin/samclip [23:10:00] Found seqtk - /usr/local/bin/seqtk [23:10:00] Found parallel - /usr/local/bin/parallel [23:10:00] Found freebayes - /usr/local/bin/freebayes [23:10:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [23:10:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [23:10:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [23:10:00] Found vcfuniq - /usr/local/bin/vcfuniq [23:10:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [23:10:00] Found gzip - /bin/gzip [23:10:00] Found vt - /usr/local/bin/vt [23:10:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [23:10:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [23:10:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [23:10:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [23:10:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [23:10:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [23:10:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [23:10:01] Please supply a reference FASTA/GBK/EMBL file with --reference
1[23:10:48] This is snippy 4.6.0
Show full stderr[23:10:48] This is snippy 4.6.0 [23:10:48] Written by Torsten Seemann [23:10:48] Obtained from https://github.com/tseemann/snippy [23:10:48] Detected operating system: linux [23:10:48] Enabling bundled linux tools. [23:10:48] Found bwa - /usr/local/bin/bwa [23:10:48] Found bcftools - /usr/local/bin/bcftools [23:10:48] Found samtools - /usr/local/bin/samtools [23:10:48] Found java - /usr/local/bin/java [23:10:48] Found snpEff - /usr/local/bin/snpEff [23:10:48] Found samclip - /usr/local/bin/samclip [23:10:48] Found seqtk - /usr/local/bin/seqtk [23:10:48] Found parallel - /usr/local/bin/parallel [23:10:48] Found freebayes - /usr/local/bin/freebayes [23:10:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [23:10:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [23:10:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [23:10:48] Found vcfuniq - /usr/local/bin/vcfuniq [23:10:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [23:10:48] Found gzip - /bin/gzip [23:10:48] Found vt - /usr/local/bin/vt [23:10:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [23:10:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [23:10:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [23:10:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [23:10:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [23:10:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [23:10:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [23:10:48] Please supply a reference FASTA/GBK/EMBL file with --reference
1[23:18:27] This is snippy 4.6.0
Show full stderr[23:18:27] This is snippy 4.6.0 [23:18:27] Written by Torsten Seemann [23:18:27] Obtained from https://github.com/tseemann/snippy [23:18:27] Detected operating system: linux [23:18:27] Enabling bundled linux tools. [23:18:27] Found bwa - /usr/local/bin/bwa [23:18:27] Found bcftools - /usr/local/bin/bcftools [23:18:27] Found samtools - /usr/local/bin/samtools [23:18:27] Found java - /usr/local/bin/java [23:18:27] Found snpEff - /usr/local/bin/snpEff [23:18:27] Found samclip - /usr/local/bin/samclip [23:18:27] Found seqtk - /usr/local/bin/seqtk [23:18:27] Found parallel - /usr/local/bin/parallel [23:18:27] Found freebayes - /usr/local/bin/freebayes [23:18:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [23:18:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [23:18:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [23:18:27] Found vcfuniq - /usr/local/bin/vcfuniq [23:18:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [23:18:27] Found gzip - /bin/gzip [23:18:27] Found vt - /usr/local/bin/vt [23:18:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [23:18:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [23:18:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [23:18:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [23:18:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [23:18:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [23:18:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [23:18:28] Please supply a reference FASTA/GBK/EMBL file with --reference
1[23:58:57] This is snippy 4.6.0
Show full stderr[23:58:57] This is snippy 4.6.0 [23:58:57] Written by Torsten Seemann [23:58:57] Obtained from https://github.com/tseemann/snippy [23:58:57] Detected operating system: linux [23:58:57] Enabling bundled linux tools. [23:58:57] Found bwa - /usr/local/bin/bwa [23:58:57] Found bcftools - /usr/local/bin/bcftools [23:58:57] Found samtools - /usr/local/bin/samtools [23:58:57] Found java - /usr/local/bin/java [23:58:57] Found snpEff - /usr/local/bin/snpEff [23:58:57] Found samclip - /usr/local/bin/samclip [23:58:57] Found seqtk - /usr/local/bin/seqtk [23:58:57] Found parallel - /usr/local/bin/parallel [23:58:57] Found freebayes - /usr/local/bin/freebayes [23:58:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [23:58:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [23:58:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [23:58:57] Found vcfuniq - /usr/local/bin/vcfuniq [23:58:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [23:58:57] Found gzip - /bin/gzip [23:58:57] Found vt - /usr/local/bin/vt [23:58:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [23:58:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [23:58:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [23:58:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [23:58:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [23:58:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [23:58:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [23:58:58] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:25:08] This is snippy 4.6.0
Show full stderr[00:25:08] This is snippy 4.6.0 [00:25:08] Written by Torsten Seemann [00:25:08] Obtained from https://github.com/tseemann/snippy [00:25:08] Detected operating system: linux [00:25:08] Enabling bundled linux tools. [00:25:08] Found bwa - /usr/local/bin/bwa [00:25:08] Found bcftools - /usr/local/bin/bcftools [00:25:08] Found samtools - /usr/local/bin/samtools [00:25:08] Found java - /usr/local/bin/java [00:25:08] Found snpEff - /usr/local/bin/snpEff [00:25:08] Found samclip - /usr/local/bin/samclip [00:25:08] Found seqtk - /usr/local/bin/seqtk [00:25:08] Found parallel - /usr/local/bin/parallel [00:25:08] Found freebayes - /usr/local/bin/freebayes [00:25:08] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:25:08] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:25:08] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:25:08] Found vcfuniq - /usr/local/bin/vcfuniq [00:25:08] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:25:08] Found gzip - /bin/gzip [00:25:08] Found vt - /usr/local/bin/vt [00:25:08] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:25:08] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:25:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:25:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:25:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:25:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:25:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:25:11] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:08:11] This is snippy 4.6.0
Show full stderr[00:08:11] This is snippy 4.6.0 [00:08:11] Written by Torsten Seemann [00:08:11] Obtained from https://github.com/tseemann/snippy [00:08:11] Detected operating system: linux [00:08:11] Enabling bundled linux tools. [00:08:11] Found bwa - /usr/local/bin/bwa [00:08:12] Found bcftools - /usr/local/bin/bcftools [00:08:12] Found samtools - /usr/local/bin/samtools [00:08:12] Found java - /usr/local/bin/java [00:08:12] Found snpEff - /usr/local/bin/snpEff [00:08:12] Found samclip - /usr/local/bin/samclip [00:08:12] Found seqtk - /usr/local/bin/seqtk [00:08:12] Found parallel - /usr/local/bin/parallel [00:08:12] Found freebayes - /usr/local/bin/freebayes [00:08:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:08:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:08:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:08:12] Found vcfuniq - /usr/local/bin/vcfuniq [00:08:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:08:12] Found gzip - /bin/gzip [00:08:12] Found vt - /usr/local/bin/vt [00:08:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:08:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:08:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:08:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:08:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:08:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:08:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:08:17] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:33:06] This is snippy 4.6.0
Show full stderr[00:33:06] This is snippy 4.6.0 [00:33:06] Written by Torsten Seemann [00:33:06] Obtained from https://github.com/tseemann/snippy [00:33:06] Detected operating system: linux [00:33:06] Enabling bundled linux tools. [00:33:06] Found bwa - /usr/local/bin/bwa [00:33:06] Found bcftools - /usr/local/bin/bcftools [00:33:06] Found samtools - /usr/local/bin/samtools [00:33:06] Found java - /usr/local/bin/java [00:33:06] Found snpEff - /usr/local/bin/snpEff [00:33:06] Found samclip - /usr/local/bin/samclip [00:33:06] Found seqtk - /usr/local/bin/seqtk [00:33:06] Found parallel - /usr/local/bin/parallel [00:33:06] Found freebayes - /usr/local/bin/freebayes [00:33:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:33:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:33:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:33:06] Found vcfuniq - /usr/local/bin/vcfuniq [00:33:06] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:33:06] Found gzip - /bin/gzip [00:33:06] Found vt - /usr/local/bin/vt [00:33:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:33:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:33:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:33:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:33:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:33:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:33:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:33:07] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:43:10] This is snippy 4.6.0
Show full stderr[00:43:10] This is snippy 4.6.0 [00:43:10] Written by Torsten Seemann [00:43:10] Obtained from https://github.com/tseemann/snippy [00:43:10] Detected operating system: linux [00:43:10] Enabling bundled linux tools. [00:43:10] Found bwa - /usr/local/bin/bwa [00:43:10] Found bcftools - /usr/local/bin/bcftools [00:43:10] Found samtools - /usr/local/bin/samtools [00:43:10] Found java - /usr/local/bin/java [00:43:10] Found snpEff - /usr/local/bin/snpEff [00:43:10] Found samclip - /usr/local/bin/samclip [00:43:10] Found seqtk - /usr/local/bin/seqtk [00:43:10] Found parallel - /usr/local/bin/parallel [00:43:10] Found freebayes - /usr/local/bin/freebayes [00:43:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:43:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:43:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:43:10] Found vcfuniq - /usr/local/bin/vcfuniq [00:43:10] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:43:10] Found gzip - /bin/gzip [00:43:10] Found vt - /usr/local/bin/vt [00:43:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:43:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:43:11] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:43:11] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:43:11] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:43:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:43:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:43:11] Please supply a reference FASTA/GBK/EMBL file with --reference
1[20:14:48] This is snippy 4.6.0
Show full stderr[20:14:48] This is snippy 4.6.0 [20:14:48] Written by Torsten Seemann [20:14:48] Obtained from https://github.com/tseemann/snippy [20:14:48] Detected operating system: linux [20:14:48] Enabling bundled linux tools. [20:14:48] Found bwa - /usr/local/bin/bwa [20:14:48] Found bcftools - /usr/local/bin/bcftools [20:14:48] Found samtools - /usr/local/bin/samtools [20:14:48] Found java - /usr/local/bin/java [20:14:48] Found snpEff - /usr/local/bin/snpEff [20:14:48] Found samclip - /usr/local/bin/samclip [20:14:48] Found seqtk - /usr/local/bin/seqtk [20:14:48] Found parallel - /usr/local/bin/parallel [20:14:48] Found freebayes - /usr/local/bin/freebayes [20:14:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [20:14:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [20:14:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [20:14:48] Found vcfuniq - /usr/local/bin/vcfuniq [20:14:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [20:14:48] Found gzip - /bin/gzip [20:14:48] Found vt - /usr/local/bin/vt [20:14:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [20:14:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [20:14:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [20:14:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [20:14:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [20:14:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [20:14:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [20:14:49] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:44:48] This is snippy 4.6.0
Show full stderr[00:44:48] This is snippy 4.6.0 [00:44:48] Written by Torsten Seemann [00:44:48] Obtained from https://github.com/tseemann/snippy [00:44:48] Detected operating system: linux [00:44:48] Enabling bundled linux tools. [00:44:48] Found bwa - /usr/local/bin/bwa [00:44:48] Found bcftools - /usr/local/bin/bcftools [00:44:48] Found samtools - /usr/local/bin/samtools [00:44:48] Found java - /usr/local/bin/java [00:44:48] Found snpEff - /usr/local/bin/snpEff [00:44:48] Found samclip - /usr/local/bin/samclip [00:44:48] Found seqtk - /usr/local/bin/seqtk [00:44:48] Found parallel - /usr/local/bin/parallel [00:44:48] Found freebayes - /usr/local/bin/freebayes [00:44:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:44:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:44:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:44:48] Found vcfuniq - /usr/local/bin/vcfuniq [00:44:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:44:48] Found gzip - /bin/gzip [00:44:48] Found vt - /usr/local/bin/vt [00:44:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:44:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:44:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:44:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:44:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:44:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:44:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:44:49] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:53:18] This is snippy 4.6.0
Show full stderr[00:53:18] This is snippy 4.6.0 [00:53:18] Written by Torsten Seemann [00:53:18] Obtained from https://github.com/tseemann/snippy [00:53:18] Detected operating system: linux [00:53:18] Enabling bundled linux tools. [00:53:18] Found bwa - /usr/local/bin/bwa [00:53:18] Found bcftools - /usr/local/bin/bcftools [00:53:18] Found samtools - /usr/local/bin/samtools [00:53:18] Found java - /usr/local/bin/java [00:53:18] Found snpEff - /usr/local/bin/snpEff [00:53:18] Found samclip - /usr/local/bin/samclip [00:53:18] Found seqtk - /usr/local/bin/seqtk [00:53:18] Found parallel - /usr/local/bin/parallel [00:53:18] Found freebayes - /usr/local/bin/freebayes [00:53:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:53:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:53:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:53:18] Found vcfuniq - /usr/local/bin/vcfuniq [00:53:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:53:18] Found gzip - /bin/gzip [00:53:18] Found vt - /usr/local/bin/vt [00:53:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:53:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:53:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:53:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:53:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:53:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:53:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:53:21] Please supply a reference FASTA/GBK/EMBL file with --reference
1[19:49:48] This is snippy 4.6.0
Show full stderr[19:49:48] This is snippy 4.6.0 [19:49:48] Written by Torsten Seemann [19:49:48] Obtained from https://github.com/tseemann/snippy [19:49:48] Detected operating system: linux [19:49:48] Enabling bundled linux tools. [19:49:48] Found bwa - /usr/local/bin/bwa [19:49:48] Found bcftools - /usr/local/bin/bcftools [19:49:48] Found samtools - /usr/local/bin/samtools [19:49:48] Found java - /usr/local/bin/java [19:49:48] Found snpEff - /usr/local/bin/snpEff [19:49:48] Found samclip - /usr/local/bin/samclip [19:49:48] Found seqtk - /usr/local/bin/seqtk [19:49:48] Found parallel - /usr/local/bin/parallel [19:49:48] Found freebayes - /usr/local/bin/freebayes [19:49:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [19:49:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [19:49:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [19:49:48] Found vcfuniq - /usr/local/bin/vcfuniq [19:49:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [19:49:48] Found gzip - /bin/gzip [19:49:48] Found vt - /usr/local/bin/vt [19:49:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [19:49:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [19:49:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [19:49:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [19:49:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [19:49:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [19:49:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [19:49:49] Please supply a reference FASTA/GBK/EMBL file with --reference
1[19:57:48] This is snippy 4.6.0
Show full stderr[19:57:48] This is snippy 4.6.0 [19:57:48] Written by Torsten Seemann [19:57:48] Obtained from https://github.com/tseemann/snippy [19:57:48] Detected operating system: linux [19:57:48] Enabling bundled linux tools. [19:57:48] Found bwa - /usr/local/bin/bwa [19:57:48] Found bcftools - /usr/local/bin/bcftools [19:57:48] Found samtools - /usr/local/bin/samtools [19:57:48] Found java - /usr/local/bin/java [19:57:48] Found snpEff - /usr/local/bin/snpEff [19:57:48] Found samclip - /usr/local/bin/samclip [19:57:48] Found seqtk - /usr/local/bin/seqtk [19:57:48] Found parallel - /usr/local/bin/parallel [19:57:48] Found freebayes - /usr/local/bin/freebayes [19:57:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [19:57:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [19:57:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [19:57:48] Found vcfuniq - /usr/local/bin/vcfuniq [19:57:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [19:57:48] Found gzip - /bin/gzip [19:57:48] Found vt - /usr/local/bin/vt [19:57:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [19:57:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [19:57:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [19:57:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [19:57:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [19:57:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [19:57:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [19:57:49] Please supply a reference FASTA/GBK/EMBL file with --reference
1[18:18:47] This is snippy 4.6.0
Show full stderr[18:18:47] This is snippy 4.6.0 [18:18:47] Written by Torsten Seemann [18:18:47] Obtained from https://github.com/tseemann/snippy [18:18:47] Detected operating system: linux [18:18:47] Enabling bundled linux tools. [18:18:47] Found bwa - /usr/local/bin/bwa [18:18:47] Found bcftools - /usr/local/bin/bcftools [18:18:47] Found samtools - /usr/local/bin/samtools [18:18:47] Found java - /usr/local/bin/java [18:18:47] Found snpEff - /usr/local/bin/snpEff [18:18:47] Found samclip - /usr/local/bin/samclip [18:18:47] Found seqtk - /usr/local/bin/seqtk [18:18:47] Found parallel - /usr/local/bin/parallel [18:18:47] Found freebayes - /usr/local/bin/freebayes [18:18:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [18:18:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [18:18:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [18:18:48] Found vcfuniq - /usr/local/bin/vcfuniq [18:18:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [18:18:48] Found gzip - /bin/gzip [18:18:48] Found vt - /usr/local/bin/vt [18:18:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [18:18:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [18:18:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [18:18:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [18:18:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [18:18:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [18:18:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [18:18:48] Please supply a reference FASTA/GBK/EMBL file with --reference
1[20:38:31] This is snippy 4.6.0
Show full stderr[20:38:31] This is snippy 4.6.0 [20:38:31] Written by Torsten Seemann [20:38:31] Obtained from https://github.com/tseemann/snippy [20:38:31] Detected operating system: linux [20:38:31] Enabling bundled linux tools. [20:38:31] Found bwa - /usr/local/bin/bwa [20:38:31] Found bcftools - /usr/local/bin/bcftools [20:38:31] Found samtools - /usr/local/bin/samtools [20:38:31] Found java - /usr/local/bin/java [20:38:31] Found snpEff - /usr/local/bin/snpEff [20:38:31] Found samclip - /usr/local/bin/samclip [20:38:31] Found seqtk - /usr/local/bin/seqtk [20:38:31] Found parallel - /usr/local/bin/parallel [20:38:31] Found freebayes - /usr/local/bin/freebayes [20:38:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [20:38:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [20:38:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [20:38:31] Found vcfuniq - /usr/local/bin/vcfuniq [20:38:31] Found vcffirstheader - /usr/local/bin/vcffirstheader [20:38:31] Found gzip - /bin/gzip [20:38:31] Found vt - /usr/local/bin/vt [20:38:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [20:38:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [20:38:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [20:38:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [20:38:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [20:38:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [20:38:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [20:38:32] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:45:17] This is snippy 4.6.0
Show full stderr[17:45:17] This is snippy 4.6.0 [17:45:17] Written by Torsten Seemann [17:45:17] Obtained from https://github.com/tseemann/snippy [17:45:17] Detected operating system: linux [17:45:17] Enabling bundled linux tools. [17:45:17] Found bwa - /usr/local/bin/bwa [17:45:17] Found bcftools - /usr/local/bin/bcftools [17:45:17] Found samtools - /usr/local/bin/samtools [17:45:17] Found java - /usr/local/bin/java [17:45:17] Found snpEff - /usr/local/bin/snpEff [17:45:17] Found samclip - /usr/local/bin/samclip [17:45:17] Found seqtk - /usr/local/bin/seqtk [17:45:17] Found parallel - /usr/local/bin/parallel [17:45:17] Found freebayes - /usr/local/bin/freebayes [17:45:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:45:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:45:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:45:17] Found vcfuniq - /usr/local/bin/vcfuniq [17:45:17] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:45:17] Found gzip - /bin/gzip [17:45:17] Found vt - /usr/local/bin/vt [17:45:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:45:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:45:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:45:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:45:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:45:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:45:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:45:18] Please supply a reference FASTA/GBK/EMBL file with --reference
1[20:38:54] This is snippy 4.6.0
Show full stderr[20:38:54] This is snippy 4.6.0 [20:38:54] Written by Torsten Seemann [20:38:54] Obtained from https://github.com/tseemann/snippy [20:38:54] Detected operating system: linux [20:38:54] Enabling bundled linux tools. [20:38:54] Found bwa - /usr/local/bin/bwa [20:38:54] Found bcftools - /usr/local/bin/bcftools [20:38:54] Found samtools - /usr/local/bin/samtools [20:38:54] Found java - /usr/local/bin/java [20:38:54] Found snpEff - /usr/local/bin/snpEff [20:38:54] Found samclip - /usr/local/bin/samclip [20:38:54] Found seqtk - /usr/local/bin/seqtk [20:38:54] Found parallel - /usr/local/bin/parallel [20:38:54] Found freebayes - /usr/local/bin/freebayes [20:38:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [20:38:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [20:38:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [20:38:54] Found vcfuniq - /usr/local/bin/vcfuniq [20:38:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [20:38:54] Found gzip - /bin/gzip [20:38:54] Found vt - /usr/local/bin/vt [20:38:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [20:38:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [20:38:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [20:38:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [20:38:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [20:38:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [20:38:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [20:38:55] Please supply a reference FASTA/GBK/EMBL file with --reference
1[21:03:39] This is snippy 4.6.0
Show full stderr[21:03:39] This is snippy 4.6.0 [21:03:39] Written by Torsten Seemann [21:03:39] Obtained from https://github.com/tseemann/snippy [21:03:39] Detected operating system: linux [21:03:39] Enabling bundled linux tools. [21:03:39] Found bwa - /usr/local/bin/bwa [21:03:39] Found bcftools - /usr/local/bin/bcftools [21:03:39] Found samtools - /usr/local/bin/samtools [21:03:39] Found java - /usr/local/bin/java [21:03:39] Found snpEff - /usr/local/bin/snpEff [21:03:39] Found samclip - /usr/local/bin/samclip [21:03:39] Found seqtk - /usr/local/bin/seqtk [21:03:39] Found parallel - /usr/local/bin/parallel [21:03:39] Found freebayes - /usr/local/bin/freebayes [21:03:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:03:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:03:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:03:39] Found vcfuniq - /usr/local/bin/vcfuniq [21:03:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:03:39] Found gzip - /bin/gzip [21:03:39] Found vt - /usr/local/bin/vt [21:03:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:03:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:03:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:03:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:03:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:03:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:03:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:03:40] Please supply a reference FASTA/GBK/EMBL file with --reference
1[21:30:47] This is snippy 4.6.0
Show full stderr[21:30:47] This is snippy 4.6.0 [21:30:47] Written by Torsten Seemann [21:30:47] Obtained from https://github.com/tseemann/snippy [21:30:47] Detected operating system: linux [21:30:47] Enabling bundled linux tools. [21:30:47] Found bwa - /usr/local/bin/bwa [21:30:47] Found bcftools - /usr/local/bin/bcftools [21:30:47] Found samtools - /usr/local/bin/samtools [21:30:47] Found java - /usr/local/bin/java [21:30:47] Found snpEff - /usr/local/bin/snpEff [21:30:47] Found samclip - /usr/local/bin/samclip [21:30:47] Found seqtk - /usr/local/bin/seqtk [21:30:47] Found parallel - /usr/local/bin/parallel [21:30:47] Found freebayes - /usr/local/bin/freebayes [21:30:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:30:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:30:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:30:47] Found vcfuniq - /usr/local/bin/vcfuniq [21:30:47] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:30:47] Found gzip - /bin/gzip [21:30:47] Found vt - /usr/local/bin/vt [21:30:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:30:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:30:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:30:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:30:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:30:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:30:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:30:48] Please supply a reference FASTA/GBK/EMBL file with --reference
1[21:55:17] This is snippy 4.6.0
Show full stderr[21:55:17] This is snippy 4.6.0 [21:55:17] Written by Torsten Seemann [21:55:17] Obtained from https://github.com/tseemann/snippy [21:55:17] Detected operating system: linux [21:55:17] Enabling bundled linux tools. [21:55:17] Found bwa - /usr/local/bin/bwa [21:55:17] Found bcftools - /usr/local/bin/bcftools [21:55:17] Found samtools - /usr/local/bin/samtools [21:55:17] Found java - /usr/local/bin/java [21:55:17] Found snpEff - /usr/local/bin/snpEff [21:55:17] Found samclip - /usr/local/bin/samclip [21:55:17] Found seqtk - /usr/local/bin/seqtk [21:55:17] Found parallel - /usr/local/bin/parallel [21:55:17] Found freebayes - /usr/local/bin/freebayes [21:55:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:55:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:55:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:55:17] Found vcfuniq - /usr/local/bin/vcfuniq [21:55:17] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:55:17] Found gzip - /bin/gzip [21:55:17] Found vt - /usr/local/bin/vt [21:55:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:55:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:55:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:55:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:55:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:55:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:55:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:55:18] Please supply a reference FASTA/GBK/EMBL file with --reference
1[22:03:04] This is snippy 4.6.0
Show full stderr[22:03:04] This is snippy 4.6.0 [22:03:04] Written by Torsten Seemann [22:03:04] Obtained from https://github.com/tseemann/snippy [22:03:04] Detected operating system: linux [22:03:04] Enabling bundled linux tools. [22:03:04] Found bwa - /usr/local/bin/bwa [22:03:04] Found bcftools - /usr/local/bin/bcftools [22:03:04] Found samtools - /usr/local/bin/samtools [22:03:04] Found java - /usr/local/bin/java [22:03:04] Found snpEff - /usr/local/bin/snpEff [22:03:04] Found samclip - /usr/local/bin/samclip [22:03:04] Found seqtk - /usr/local/bin/seqtk [22:03:04] Found parallel - /usr/local/bin/parallel [22:03:04] Found freebayes - /usr/local/bin/freebayes [22:03:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [22:03:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [22:03:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [22:03:04] Found vcfuniq - /usr/local/bin/vcfuniq [22:03:04] Found vcffirstheader - /usr/local/bin/vcffirstheader [22:03:04] Found gzip - /bin/gzip [22:03:04] Found vt - /usr/local/bin/vt [22:03:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [22:03:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [22:03:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [22:03:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [22:03:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [22:03:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [22:03:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [22:03:05] Please supply a reference FASTA/GBK/EMBL file with --reference
1[22:11:47] This is snippy 4.6.0
Show full stderr[22:11:47] This is snippy 4.6.0 [22:11:47] Written by Torsten Seemann [22:11:47] Obtained from https://github.com/tseemann/snippy [22:11:47] Detected operating system: linux [22:11:47] Enabling bundled linux tools. [22:11:47] Found bwa - /usr/local/bin/bwa [22:11:47] Found bcftools - /usr/local/bin/bcftools [22:11:47] Found samtools - /usr/local/bin/samtools [22:11:47] Found java - /usr/local/bin/java [22:11:47] Found snpEff - /usr/local/bin/snpEff [22:11:47] Found samclip - /usr/local/bin/samclip [22:11:47] Found seqtk - /usr/local/bin/seqtk [22:11:47] Found parallel - /usr/local/bin/parallel [22:11:47] Found freebayes - /usr/local/bin/freebayes [22:11:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [22:11:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [22:11:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [22:11:47] Found vcfuniq - /usr/local/bin/vcfuniq [22:11:47] Found vcffirstheader - /usr/local/bin/vcffirstheader [22:11:47] Found gzip - /bin/gzip [22:11:47] Found vt - /usr/local/bin/vt [22:11:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [22:11:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [22:11:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [22:11:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [22:11:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [22:11:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [22:11:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [22:11:48] Please supply a reference FASTA/GBK/EMBL file with --reference
1[22:19:30] This is snippy 4.6.0
Show full stderr[22:19:30] This is snippy 4.6.0 [22:19:30] Written by Torsten Seemann [22:19:30] Obtained from https://github.com/tseemann/snippy [22:19:30] Detected operating system: linux [22:19:30] Enabling bundled linux tools. [22:19:30] Found bwa - /usr/local/bin/bwa [22:19:30] Found bcftools - /usr/local/bin/bcftools [22:19:30] Found samtools - /usr/local/bin/samtools [22:19:30] Found java - /usr/local/bin/java [22:19:30] Found snpEff - /usr/local/bin/snpEff [22:19:30] Found samclip - /usr/local/bin/samclip [22:19:30] Found seqtk - /usr/local/bin/seqtk [22:19:30] Found parallel - /usr/local/bin/parallel [22:19:30] Found freebayes - /usr/local/bin/freebayes [22:19:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [22:19:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [22:19:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [22:19:31] Found vcfuniq - /usr/local/bin/vcfuniq [22:19:31] Found vcffirstheader - /usr/local/bin/vcffirstheader [22:19:31] Found gzip - /bin/gzip [22:19:31] Found vt - /usr/local/bin/vt [22:19:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [22:19:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [22:19:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [22:19:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [22:19:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [22:19:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [22:19:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [22:19:31] Please supply a reference FASTA/GBK/EMBL file with --reference
1[22:37:17] This is snippy 4.6.0
Show full stderr[22:37:17] This is snippy 4.6.0 [22:37:17] Written by Torsten Seemann [22:37:17] Obtained from https://github.com/tseemann/snippy [22:37:17] Detected operating system: linux [22:37:17] Enabling bundled linux tools. [22:37:17] Found bwa - /usr/local/bin/bwa [22:37:17] Found bcftools - /usr/local/bin/bcftools [22:37:17] Found samtools - /usr/local/bin/samtools [22:37:17] Found java - /usr/local/bin/java [22:37:17] Found snpEff - /usr/local/bin/snpEff [22:37:17] Found samclip - /usr/local/bin/samclip [22:37:17] Found seqtk - /usr/local/bin/seqtk [22:37:17] Found parallel - /usr/local/bin/parallel [22:37:17] Found freebayes - /usr/local/bin/freebayes [22:37:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [22:37:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [22:37:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [22:37:17] Found vcfuniq - /usr/local/bin/vcfuniq [22:37:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [22:37:18] Found gzip - /bin/gzip [22:37:18] Found vt - /usr/local/bin/vt [22:37:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [22:37:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [22:37:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [22:37:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [22:37:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [22:37:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [22:37:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [22:37:18] Please supply a reference FASTA/GBK/EMBL file with --reference
1[20:54:58] This is snippy 4.6.0
Show full stderr[20:54:58] This is snippy 4.6.0 [20:54:58] Written by Torsten Seemann [20:54:58] Obtained from https://github.com/tseemann/snippy [20:54:58] Detected operating system: linux [20:54:58] Enabling bundled linux tools. [20:54:58] Found bwa - /usr/local/bin/bwa [20:54:58] Found bcftools - /usr/local/bin/bcftools [20:54:58] Found samtools - /usr/local/bin/samtools [20:54:58] Found java - /usr/local/bin/java [20:54:58] Found snpEff - /usr/local/bin/snpEff [20:54:58] Found samclip - /usr/local/bin/samclip [20:54:58] Found seqtk - /usr/local/bin/seqtk [20:54:58] Found parallel - /usr/local/bin/parallel [20:54:58] Found freebayes - /usr/local/bin/freebayes [20:54:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [20:54:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [20:54:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [20:54:58] Found vcfuniq - /usr/local/bin/vcfuniq [20:54:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [20:54:58] Found gzip - /bin/gzip [20:54:58] Found vt - /usr/local/bin/vt [20:54:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [20:54:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [20:54:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [20:54:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [20:54:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [20:54:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [20:54:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [20:54:59] Please supply a reference FASTA/GBK/EMBL file with --reference
1[20:55:48] This is snippy 4.6.0
Show full stderr[20:55:48] This is snippy 4.6.0 [20:55:48] Written by Torsten Seemann [20:55:48] Obtained from https://github.com/tseemann/snippy [20:55:48] Detected operating system: linux [20:55:48] Enabling bundled linux tools. [20:55:48] Found bwa - /usr/local/bin/bwa [20:55:48] Found bcftools - /usr/local/bin/bcftools [20:55:48] Found samtools - /usr/local/bin/samtools [20:55:48] Found java - /usr/local/bin/java [20:55:48] Found snpEff - /usr/local/bin/snpEff [20:55:48] Found samclip - /usr/local/bin/samclip [20:55:48] Found seqtk - /usr/local/bin/seqtk [20:55:48] Found parallel - /usr/local/bin/parallel [20:55:48] Found freebayes - /usr/local/bin/freebayes [20:55:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [20:55:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [20:55:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [20:55:48] Found vcfuniq - /usr/local/bin/vcfuniq [20:55:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [20:55:48] Found gzip - /bin/gzip [20:55:48] Found vt - /usr/local/bin/vt [20:55:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [20:55:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [20:55:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [20:55:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [20:55:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [20:55:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [20:55:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [20:55:50] Please supply a reference FASTA/GBK/EMBL file with --reference
1[21:19:59] This is snippy 4.6.0
Show full stderr[21:19:59] This is snippy 4.6.0 [21:19:59] Written by Torsten Seemann [21:19:59] Obtained from https://github.com/tseemann/snippy [21:19:59] Detected operating system: linux [21:19:59] Enabling bundled linux tools. [21:19:59] Found bwa - /usr/local/bin/bwa [21:19:59] Found bcftools - /usr/local/bin/bcftools [21:19:59] Found samtools - /usr/local/bin/samtools [21:19:59] Found java - /usr/local/bin/java [21:19:59] Found snpEff - /usr/local/bin/snpEff [21:19:59] Found samclip - /usr/local/bin/samclip [21:19:59] Found seqtk - /usr/local/bin/seqtk [21:19:59] Found parallel - /usr/local/bin/parallel [21:19:59] Found freebayes - /usr/local/bin/freebayes [21:19:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:19:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:19:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:19:59] Found vcfuniq - /usr/local/bin/vcfuniq [21:19:59] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:19:59] Found gzip - /bin/gzip [21:19:59] Found vt - /usr/local/bin/vt [21:19:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:19:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:19:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:19:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:19:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:20:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:20:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:20:00] Please supply a reference FASTA/GBK/EMBL file with --reference
1[19:24:00] This is snippy 4.6.0
Show full stderr[19:24:00] This is snippy 4.6.0 [19:24:00] Written by Torsten Seemann [19:24:00] Obtained from https://github.com/tseemann/snippy [19:24:00] Detected operating system: linux [19:24:00] Enabling bundled linux tools. [19:24:00] Found bwa - /usr/local/bin/bwa [19:24:00] Found bcftools - /usr/local/bin/bcftools [19:24:00] Found samtools - /usr/local/bin/samtools [19:24:00] Found java - /usr/local/bin/java [19:24:00] Found snpEff - /usr/local/bin/snpEff [19:24:00] Found samclip - /usr/local/bin/samclip [19:24:00] Found seqtk - /usr/local/bin/seqtk [19:24:00] Found parallel - /usr/local/bin/parallel [19:24:00] Found freebayes - /usr/local/bin/freebayes [19:24:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [19:24:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [19:24:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [19:24:00] Found vcfuniq - /usr/local/bin/vcfuniq [19:24:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [19:24:00] Found gzip - /bin/gzip [19:24:00] Found vt - /usr/local/bin/vt [19:24:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [19:24:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [19:24:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [19:24:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [19:24:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [19:24:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [19:24:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [19:24:01] Please supply a reference FASTA/GBK/EMBL file with --reference
1[21:21:22] This is snippy 4.6.0
Show full stderr[21:21:22] This is snippy 4.6.0 [21:21:22] Written by Torsten Seemann [21:21:22] Obtained from https://github.com/tseemann/snippy [21:21:22] Detected operating system: linux [21:21:22] Enabling bundled linux tools. [21:21:22] Found bwa - /usr/local/bin/bwa [21:21:22] Found bcftools - /usr/local/bin/bcftools [21:21:22] Found samtools - /usr/local/bin/samtools [21:21:22] Found java - /usr/local/bin/java [21:21:22] Found snpEff - /usr/local/bin/snpEff [21:21:22] Found samclip - /usr/local/bin/samclip [21:21:22] Found seqtk - /usr/local/bin/seqtk [21:21:22] Found parallel - /usr/local/bin/parallel [21:21:22] Found freebayes - /usr/local/bin/freebayes [21:21:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:21:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:21:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:21:22] Found vcfuniq - /usr/local/bin/vcfuniq [21:21:22] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:21:22] Found gzip - /bin/gzip [21:21:22] Found vt - /usr/local/bin/vt [21:21:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:21:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:21:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:21:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:21:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:21:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:21:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:21:23] Please supply a reference FASTA/GBK/EMBL file with --reference
1[21:20:12] This is snippy 4.6.0
Show full stderr[21:20:12] This is snippy 4.6.0 [21:20:12] Written by Torsten Seemann [21:20:12] Obtained from https://github.com/tseemann/snippy [21:20:12] Detected operating system: linux [21:20:12] Enabling bundled linux tools. [21:20:12] Found bwa - /usr/local/bin/bwa [21:20:12] Found bcftools - /usr/local/bin/bcftools [21:20:12] Found samtools - /usr/local/bin/samtools [21:20:12] Found java - /usr/local/bin/java [21:20:12] Found snpEff - /usr/local/bin/snpEff [21:20:12] Found samclip - /usr/local/bin/samclip [21:20:12] Found seqtk - /usr/local/bin/seqtk [21:20:12] Found parallel - /usr/local/bin/parallel [21:20:12] Found freebayes - /usr/local/bin/freebayes [21:20:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:20:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:20:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:20:12] Found vcfuniq - /usr/local/bin/vcfuniq [21:20:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:20:12] Found gzip - /bin/gzip [21:20:12] Found vt - /usr/local/bin/vt [21:20:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:20:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:20:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:20:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:20:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:20:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:20:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:20:13] Please supply a reference FASTA/GBK/EMBL file with --reference
1[21:29:59] This is snippy 4.6.0
Show full stderr[21:29:59] This is snippy 4.6.0 [21:29:59] Written by Torsten Seemann [21:29:59] Obtained from https://github.com/tseemann/snippy [21:29:59] Detected operating system: linux [21:29:59] Enabling bundled linux tools. [21:29:59] Found bwa - /usr/local/bin/bwa [21:29:59] Found bcftools - /usr/local/bin/bcftools [21:29:59] Found samtools - /usr/local/bin/samtools [21:29:59] Found java - /usr/local/bin/java [21:29:59] Found snpEff - /usr/local/bin/snpEff [21:29:59] Found samclip - /usr/local/bin/samclip [21:29:59] Found seqtk - /usr/local/bin/seqtk [21:29:59] Found parallel - /usr/local/bin/parallel [21:29:59] Found freebayes - /usr/local/bin/freebayes [21:29:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:29:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:29:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:29:59] Found vcfuniq - /usr/local/bin/vcfuniq [21:29:59] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:29:59] Found gzip - /bin/gzip [21:29:59] Found vt - /usr/local/bin/vt [21:29:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:29:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:29:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:29:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:29:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:30:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:30:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:30:00] Please supply a reference FASTA/GBK/EMBL file with --reference
1[21:38:27] This is snippy 4.6.0
Show full stderr[21:38:27] This is snippy 4.6.0 [21:38:27] Written by Torsten Seemann [21:38:27] Obtained from https://github.com/tseemann/snippy [21:38:27] Detected operating system: linux [21:38:27] Enabling bundled linux tools. [21:38:27] Found bwa - /usr/local/bin/bwa [21:38:27] Found bcftools - /usr/local/bin/bcftools [21:38:27] Found samtools - /usr/local/bin/samtools [21:38:27] Found java - /usr/local/bin/java [21:38:27] Found snpEff - /usr/local/bin/snpEff [21:38:27] Found samclip - /usr/local/bin/samclip [21:38:28] Found seqtk - /usr/local/bin/seqtk [21:38:28] Found parallel - /usr/local/bin/parallel [21:38:28] Found freebayes - /usr/local/bin/freebayes [21:38:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:38:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:38:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:38:28] Found vcfuniq - /usr/local/bin/vcfuniq [21:38:28] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:38:28] Found gzip - /bin/gzip [21:38:28] Found vt - /usr/local/bin/vt [21:38:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:38:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:38:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:38:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:38:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:38:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:38:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:38:29] Please supply a reference FASTA/GBK/EMBL file with --reference
1[21:46:28] This is snippy 4.6.0
Show full stderr[21:46:28] This is snippy 4.6.0 [21:46:28] Written by Torsten Seemann [21:46:28] Obtained from https://github.com/tseemann/snippy [21:46:28] Detected operating system: linux [21:46:28] Enabling bundled linux tools. [21:46:28] Found bwa - /usr/local/bin/bwa [21:46:28] Found bcftools - /usr/local/bin/bcftools [21:46:28] Found samtools - /usr/local/bin/samtools [21:46:28] Found java - /usr/local/bin/java [21:46:28] Found snpEff - /usr/local/bin/snpEff [21:46:28] Found samclip - /usr/local/bin/samclip [21:46:28] Found seqtk - /usr/local/bin/seqtk [21:46:28] Found parallel - /usr/local/bin/parallel [21:46:28] Found freebayes - /usr/local/bin/freebayes [21:46:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:46:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:46:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:46:28] Found vcfuniq - /usr/local/bin/vcfuniq [21:46:28] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:46:28] Found gzip - /bin/gzip [21:46:28] Found vt - /usr/local/bin/vt [21:46:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:46:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:46:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:46:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:46:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:46:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:46:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:46:29] Please supply a reference FASTA/GBK/EMBL file with --reference
1[21:46:47] This is snippy 4.6.0
Show full stderr[21:46:47] This is snippy 4.6.0 [21:46:47] Written by Torsten Seemann [21:46:47] Obtained from https://github.com/tseemann/snippy [21:46:47] Detected operating system: linux [21:46:47] Enabling bundled linux tools. [21:46:47] Found bwa - /usr/local/bin/bwa [21:46:47] Found bcftools - /usr/local/bin/bcftools [21:46:47] Found samtools - /usr/local/bin/samtools [21:46:47] Found java - /usr/local/bin/java [21:46:47] Found snpEff - /usr/local/bin/snpEff [21:46:47] Found samclip - /usr/local/bin/samclip [21:46:47] Found seqtk - /usr/local/bin/seqtk [21:46:47] Found parallel - /usr/local/bin/parallel [21:46:47] Found freebayes - /usr/local/bin/freebayes [21:46:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:46:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:46:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:46:47] Found vcfuniq - /usr/local/bin/vcfuniq [21:46:47] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:46:47] Found gzip - /bin/gzip [21:46:47] Found vt - /usr/local/bin/vt [21:46:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:46:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:46:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:46:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:46:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:46:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:46:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:46:48] Please supply a reference FASTA/GBK/EMBL file with --reference
1[21:54:29] This is snippy 4.6.0
Show full stderr[21:54:29] This is snippy 4.6.0 [21:54:29] Written by Torsten Seemann [21:54:29] Obtained from https://github.com/tseemann/snippy [21:54:29] Detected operating system: linux [21:54:29] Enabling bundled linux tools. [21:54:29] Found bwa - /usr/local/bin/bwa [21:54:29] Found bcftools - /usr/local/bin/bcftools [21:54:29] Found samtools - /usr/local/bin/samtools [21:54:29] Found java - /usr/local/bin/java [21:54:29] Found snpEff - /usr/local/bin/snpEff [21:54:29] Found samclip - /usr/local/bin/samclip [21:54:29] Found seqtk - /usr/local/bin/seqtk [21:54:29] Found parallel - /usr/local/bin/parallel [21:54:29] Found freebayes - /usr/local/bin/freebayes [21:54:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:54:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:54:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:54:29] Found vcfuniq - /usr/local/bin/vcfuniq [21:54:29] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:54:29] Found gzip - /bin/gzip [21:54:29] Found vt - /usr/local/bin/vt [21:54:29] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:54:29] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:54:29] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:54:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:54:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:54:30] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:54:30] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:54:30] Please supply a reference FASTA/GBK/EMBL file with --reference
1[22:28:00] This is snippy 4.6.0
Show full stderr[22:28:00] This is snippy 4.6.0 [22:28:00] Written by Torsten Seemann [22:28:00] Obtained from https://github.com/tseemann/snippy [22:28:00] Detected operating system: linux [22:28:00] Enabling bundled linux tools. [22:28:00] Found bwa - /usr/local/bin/bwa [22:28:00] Found bcftools - /usr/local/bin/bcftools [22:28:00] Found samtools - /usr/local/bin/samtools [22:28:00] Found java - /usr/local/bin/java [22:28:00] Found snpEff - /usr/local/bin/snpEff [22:28:00] Found samclip - /usr/local/bin/samclip [22:28:00] Found seqtk - /usr/local/bin/seqtk [22:28:00] Found parallel - /usr/local/bin/parallel [22:28:00] Found freebayes - /usr/local/bin/freebayes [22:28:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [22:28:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [22:28:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [22:28:00] Found vcfuniq - /usr/local/bin/vcfuniq [22:28:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [22:28:00] Found gzip - /bin/gzip [22:28:00] Found vt - /usr/local/bin/vt [22:28:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [22:28:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [22:28:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [22:28:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [22:28:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [22:28:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [22:28:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [22:28:01] Please supply a reference FASTA/GBK/EMBL file with --reference
1[22:28:29] This is snippy 4.6.0
Show full stderr[22:28:29] This is snippy 4.6.0 [22:28:29] Written by Torsten Seemann [22:28:29] Obtained from https://github.com/tseemann/snippy [22:28:29] Detected operating system: linux [22:28:29] Enabling bundled linux tools. [22:28:29] Found bwa - /usr/local/bin/bwa [22:28:29] Found bcftools - /usr/local/bin/bcftools [22:28:29] Found samtools - /usr/local/bin/samtools [22:28:29] Found java - /usr/local/bin/java [22:28:29] Found snpEff - /usr/local/bin/snpEff [22:28:29] Found samclip - /usr/local/bin/samclip [22:28:29] Found seqtk - /usr/local/bin/seqtk [22:28:29] Found parallel - /usr/local/bin/parallel [22:28:29] Found freebayes - /usr/local/bin/freebayes [22:28:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [22:28:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [22:28:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [22:28:29] Found vcfuniq - /usr/local/bin/vcfuniq [22:28:29] Found vcffirstheader - /usr/local/bin/vcffirstheader [22:28:29] Found gzip - /bin/gzip [22:28:29] Found vt - /usr/local/bin/vt [22:28:29] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [22:28:29] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [22:28:29] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [22:28:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [22:28:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [22:28:30] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [22:28:30] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [22:28:30] Please supply a reference FASTA/GBK/EMBL file with --reference
1[23:01:35] This is snippy 4.6.0
Show full stderr[23:01:35] This is snippy 4.6.0 [23:01:35] Written by Torsten Seemann [23:01:35] Obtained from https://github.com/tseemann/snippy [23:01:35] Detected operating system: linux [23:01:35] Enabling bundled linux tools. [23:01:35] Found bwa - /usr/local/bin/bwa [23:01:35] Found bcftools - /usr/local/bin/bcftools [23:01:35] Found samtools - /usr/local/bin/samtools [23:01:35] Found java - /usr/local/bin/java [23:01:35] Found snpEff - /usr/local/bin/snpEff [23:01:35] Found samclip - /usr/local/bin/samclip [23:01:35] Found seqtk - /usr/local/bin/seqtk [23:01:35] Found parallel - /usr/local/bin/parallel [23:01:35] Found freebayes - /usr/local/bin/freebayes [23:01:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [23:01:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [23:01:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [23:01:35] Found vcfuniq - /usr/local/bin/vcfuniq [23:01:35] Found vcffirstheader - /usr/local/bin/vcffirstheader [23:01:35] Found gzip - /bin/gzip [23:01:35] Found vt - /usr/local/bin/vt [23:01:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [23:01:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [23:01:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [23:01:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [23:01:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [23:01:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [23:01:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [23:01:36] Please supply a reference FASTA/GBK/EMBL file with --reference
1[23:01:50] This is snippy 4.6.0
Show full stderr[23:01:50] This is snippy 4.6.0 [23:01:50] Written by Torsten Seemann [23:01:50] Obtained from https://github.com/tseemann/snippy [23:01:50] Detected operating system: linux [23:01:50] Enabling bundled linux tools. [23:01:50] Found bwa - /usr/local/bin/bwa [23:01:50] Found bcftools - /usr/local/bin/bcftools [23:01:50] Found samtools - /usr/local/bin/samtools [23:01:50] Found java - /usr/local/bin/java [23:01:50] Found snpEff - /usr/local/bin/snpEff [23:01:50] Found samclip - /usr/local/bin/samclip [23:01:50] Found seqtk - /usr/local/bin/seqtk [23:01:50] Found parallel - /usr/local/bin/parallel [23:01:50] Found freebayes - /usr/local/bin/freebayes [23:01:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [23:01:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [23:01:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [23:01:50] Found vcfuniq - /usr/local/bin/vcfuniq [23:01:50] Found vcffirstheader - /usr/local/bin/vcffirstheader [23:01:50] Found gzip - /bin/gzip [23:01:50] Found vt - /usr/local/bin/vt [23:01:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [23:01:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [23:01:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [23:01:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [23:01:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [23:01:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [23:01:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [23:01:51] Please supply a reference FASTA/GBK/EMBL file with --reference
1[02:00:10] This is snippy 4.6.0
Show full stderr[02:00:10] This is snippy 4.6.0 [02:00:10] Written by Torsten Seemann [02:00:10] Obtained from https://github.com/tseemann/snippy [02:00:10] Detected operating system: linux [02:00:10] Enabling bundled linux tools. [02:00:10] Found bwa - /usr/local/bin/bwa [02:00:10] Found bcftools - /usr/local/bin/bcftools [02:00:10] Found samtools - /usr/local/bin/samtools [02:00:10] Found java - /usr/local/bin/java [02:00:10] Found snpEff - /usr/local/bin/snpEff [02:00:10] Found samclip - /usr/local/bin/samclip [02:00:10] Found seqtk - /usr/local/bin/seqtk [02:00:10] Found parallel - /usr/local/bin/parallel [02:00:10] Found freebayes - /usr/local/bin/freebayes [02:00:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [02:00:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [02:00:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [02:00:10] Found vcfuniq - /usr/local/bin/vcfuniq [02:00:10] Found vcffirstheader - /usr/local/bin/vcffirstheader [02:00:10] Found gzip - /bin/gzip [02:00:10] Found vt - /usr/local/bin/vt [02:00:11] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [02:00:11] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [02:00:11] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [02:00:11] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [02:00:11] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [02:00:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [02:00:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [02:00:11] Please supply a reference FASTA/GBK/EMBL file with --reference
1[18:51:18] This is snippy 4.6.0
Show full stderr[18:51:18] This is snippy 4.6.0 [18:51:18] Written by Torsten Seemann [18:51:18] Obtained from https://github.com/tseemann/snippy [18:51:18] Detected operating system: linux [18:51:18] Enabling bundled linux tools. [18:51:18] Found bwa - /usr/local/bin/bwa [18:51:18] Found bcftools - /usr/local/bin/bcftools [18:51:18] Found samtools - /usr/local/bin/samtools [18:51:18] Found java - /usr/local/bin/java [18:51:18] Found snpEff - /usr/local/bin/snpEff [18:51:18] Found samclip - /usr/local/bin/samclip [18:51:18] Found seqtk - /usr/local/bin/seqtk [18:51:18] Found parallel - /usr/local/bin/parallel [18:51:18] Found freebayes - /usr/local/bin/freebayes [18:51:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [18:51:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [18:51:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [18:51:18] Found vcfuniq - /usr/local/bin/vcfuniq [18:51:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [18:51:18] Found gzip - /bin/gzip [18:51:18] Found vt - /usr/local/bin/vt [18:51:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [18:51:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [18:51:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [18:51:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [18:51:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [18:51:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [18:51:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [18:51:18] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:17:23] This is snippy 4.6.0
Show full stderr[17:17:23] This is snippy 4.6.0 [17:17:23] Written by Torsten Seemann [17:17:23] Obtained from https://github.com/tseemann/snippy [17:17:23] Detected operating system: linux [17:17:23] Enabling bundled linux tools. [17:17:23] Found bwa - /usr/local/bin/bwa [17:17:23] Found bcftools - /usr/local/bin/bcftools [17:17:23] Found samtools - /usr/local/bin/samtools [17:17:23] Found java - /usr/local/bin/java [17:17:23] Found snpEff - /usr/local/bin/snpEff [17:17:23] Found samclip - /usr/local/bin/samclip [17:17:23] Found seqtk - /usr/local/bin/seqtk [17:17:23] Found parallel - /usr/local/bin/parallel [17:17:23] Found freebayes - /usr/local/bin/freebayes [17:17:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:17:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:17:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:17:23] Found vcfuniq - /usr/local/bin/vcfuniq [17:17:23] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:17:23] Found gzip - /bin/gzip [17:17:23] Found vt - /usr/local/bin/vt [17:17:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:17:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:17:23] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:17:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:17:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:17:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:17:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:17:24] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:17:12] This is snippy 4.6.0
Show full stderr[17:17:12] This is snippy 4.6.0 [17:17:12] Written by Torsten Seemann [17:17:12] Obtained from https://github.com/tseemann/snippy [17:17:12] Detected operating system: linux [17:17:12] Enabling bundled linux tools. [17:17:12] Found bwa - /usr/local/bin/bwa [17:17:12] Found bcftools - /usr/local/bin/bcftools [17:17:12] Found samtools - /usr/local/bin/samtools [17:17:12] Found java - /usr/local/bin/java [17:17:12] Found snpEff - /usr/local/bin/snpEff [17:17:12] Found samclip - /usr/local/bin/samclip [17:17:12] Found seqtk - /usr/local/bin/seqtk [17:17:12] Found parallel - /usr/local/bin/parallel [17:17:12] Found freebayes - /usr/local/bin/freebayes [17:17:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:17:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:17:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:17:12] Found vcfuniq - /usr/local/bin/vcfuniq [17:17:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:17:12] Found gzip - /bin/gzip [17:17:12] Found vt - /usr/local/bin/vt [17:17:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:17:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:17:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:17:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:17:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:17:12] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:17:12] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:17:12] Please supply a reference FASTA/GBK/EMBL file with --reference
1[02:00:26] This is snippy 4.6.0
Show full stderr[02:00:26] This is snippy 4.6.0 [02:00:26] Written by Torsten Seemann [02:00:26] Obtained from https://github.com/tseemann/snippy [02:00:26] Detected operating system: linux [02:00:26] Enabling bundled linux tools. [02:00:26] Found bwa - /usr/local/bin/bwa [02:00:26] Found bcftools - /usr/local/bin/bcftools [02:00:26] Found samtools - /usr/local/bin/samtools [02:00:26] Found java - /usr/local/bin/java [02:00:26] Found snpEff - /usr/local/bin/snpEff [02:00:26] Found samclip - /usr/local/bin/samclip [02:00:26] Found seqtk - /usr/local/bin/seqtk [02:00:26] Found parallel - /usr/local/bin/parallel [02:00:26] Found freebayes - /usr/local/bin/freebayes [02:00:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [02:00:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [02:00:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [02:00:26] Found vcfuniq - /usr/local/bin/vcfuniq [02:00:26] Found vcffirstheader - /usr/local/bin/vcffirstheader [02:00:26] Found gzip - /bin/gzip [02:00:26] Found vt - /usr/local/bin/vt [02:00:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [02:00:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [02:00:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [02:00:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [02:00:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [02:00:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [02:00:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [02:00:27] Please supply a reference FASTA/GBK/EMBL file with --reference
1[21:03:27] This is snippy 4.6.0
Show full stderr[21:03:27] This is snippy 4.6.0 [21:03:27] Written by Torsten Seemann [21:03:27] Obtained from https://github.com/tseemann/snippy [21:03:27] Detected operating system: linux [21:03:27] Enabling bundled linux tools. [21:03:27] Found bwa - /usr/local/bin/bwa [21:03:27] Found bcftools - /usr/local/bin/bcftools [21:03:27] Found samtools - /usr/local/bin/samtools [21:03:27] Found java - /usr/local/bin/java [21:03:27] Found snpEff - /usr/local/bin/snpEff [21:03:27] Found samclip - /usr/local/bin/samclip [21:03:27] Found seqtk - /usr/local/bin/seqtk [21:03:27] Found parallel - /usr/local/bin/parallel [21:03:27] Found freebayes - /usr/local/bin/freebayes [21:03:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:03:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:03:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:03:27] Found vcfuniq - /usr/local/bin/vcfuniq [21:03:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:03:27] Found gzip - /bin/gzip [21:03:27] Found vt - /usr/local/bin/vt [21:03:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:03:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:03:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:03:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:03:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:03:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:03:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:03:28] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:44:05] This is snippy 4.6.0
Show full stderr[00:44:05] This is snippy 4.6.0 [00:44:05] Written by Torsten Seemann [00:44:05] Obtained from https://github.com/tseemann/snippy [00:44:05] Detected operating system: linux [00:44:05] Enabling bundled linux tools. [00:44:05] Found bwa - /usr/local/bin/bwa [00:44:05] Found bcftools - /usr/local/bin/bcftools [00:44:05] Found samtools - /usr/local/bin/samtools [00:44:05] Found java - /usr/local/bin/java [00:44:05] Found snpEff - /usr/local/bin/snpEff [00:44:05] Found samclip - /usr/local/bin/samclip [00:44:05] Found seqtk - /usr/local/bin/seqtk [00:44:05] Found parallel - /usr/local/bin/parallel [00:44:05] Found freebayes - /usr/local/bin/freebayes [00:44:05] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:44:05] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:44:05] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:44:05] Found vcfuniq - /usr/local/bin/vcfuniq [00:44:05] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:44:05] Found gzip - /bin/gzip [00:44:05] Found vt - /usr/local/bin/vt [00:44:05] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:44:05] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:44:05] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:44:05] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:44:05] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:44:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:44:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:44:06] Please supply a reference FASTA/GBK/EMBL file with --reference
1[02:00:48] This is snippy 4.6.0
Show full stderr[02:00:48] This is snippy 4.6.0 [02:00:48] Written by Torsten Seemann [02:00:48] Obtained from https://github.com/tseemann/snippy [02:00:48] Detected operating system: linux [02:00:48] Enabling bundled linux tools. [02:00:48] Found bwa - /usr/local/bin/bwa [02:00:48] Found bcftools - /usr/local/bin/bcftools [02:00:48] Found samtools - /usr/local/bin/samtools [02:00:48] Found java - /usr/local/bin/java [02:00:48] Found snpEff - /usr/local/bin/snpEff [02:00:48] Found samclip - /usr/local/bin/samclip [02:00:48] Found seqtk - /usr/local/bin/seqtk [02:00:48] Found parallel - /usr/local/bin/parallel [02:00:48] Found freebayes - /usr/local/bin/freebayes [02:00:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [02:00:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [02:00:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [02:00:48] Found vcfuniq - /usr/local/bin/vcfuniq [02:00:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [02:00:48] Found gzip - /bin/gzip [02:00:48] Found vt - /usr/local/bin/vt [02:00:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [02:00:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [02:00:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [02:00:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [02:00:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [02:00:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [02:00:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [02:00:49] Please supply a reference FASTA/GBK/EMBL file with --reference
1[21:04:17] This is snippy 4.6.0
Show full stderr[21:04:17] This is snippy 4.6.0 [21:04:17] Written by Torsten Seemann [21:04:17] Obtained from https://github.com/tseemann/snippy [21:04:17] Detected operating system: linux [21:04:17] Enabling bundled linux tools. [21:04:17] Found bwa - /usr/local/bin/bwa [21:04:17] Found bcftools - /usr/local/bin/bcftools [21:04:17] Found samtools - /usr/local/bin/samtools [21:04:17] Found java - /usr/local/bin/java [21:04:17] Found snpEff - /usr/local/bin/snpEff [21:04:18] Found samclip - /usr/local/bin/samclip [21:04:18] Found seqtk - /usr/local/bin/seqtk [21:04:18] Found parallel - /usr/local/bin/parallel [21:04:18] Found freebayes - /usr/local/bin/freebayes [21:04:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:04:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:04:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:04:18] Found vcfuniq - /usr/local/bin/vcfuniq [21:04:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:04:18] Found gzip - /bin/gzip [21:04:18] Found vt - /usr/local/bin/vt [21:04:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:04:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:04:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:04:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:04:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:04:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:04:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:04:18] Please supply a reference FASTA/GBK/EMBL file with --reference
1[21:38:47] This is snippy 4.6.0
Show full stderr[21:38:47] This is snippy 4.6.0 [21:38:47] Written by Torsten Seemann [21:38:47] Obtained from https://github.com/tseemann/snippy [21:38:47] Detected operating system: linux [21:38:47] Enabling bundled linux tools. [21:38:47] Found bwa - /usr/local/bin/bwa [21:38:47] Found bcftools - /usr/local/bin/bcftools [21:38:47] Found samtools - /usr/local/bin/samtools [21:38:47] Found java - /usr/local/bin/java [21:38:47] Found snpEff - /usr/local/bin/snpEff [21:38:47] Found samclip - /usr/local/bin/samclip [21:38:47] Found seqtk - /usr/local/bin/seqtk [21:38:47] Found parallel - /usr/local/bin/parallel [21:38:47] Found freebayes - /usr/local/bin/freebayes [21:38:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:38:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:38:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:38:47] Found vcfuniq - /usr/local/bin/vcfuniq [21:38:47] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:38:47] Found gzip - /bin/gzip [21:38:47] Found vt - /usr/local/bin/vt [21:38:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:38:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:38:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:38:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:38:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:38:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:38:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:38:48] Please supply a reference FASTA/GBK/EMBL file with --reference
1[23:01:16] This is snippy 4.6.0
Show full stderr[23:01:16] This is snippy 4.6.0 [23:01:16] Written by Torsten Seemann [23:01:16] Obtained from https://github.com/tseemann/snippy [23:01:16] Detected operating system: linux [23:01:16] Enabling bundled linux tools. [23:01:16] Found bwa - /usr/local/bin/bwa [23:01:16] Found bcftools - /usr/local/bin/bcftools [23:01:16] Found samtools - /usr/local/bin/samtools [23:01:16] Found java - /usr/local/bin/java [23:01:16] Found snpEff - /usr/local/bin/snpEff [23:01:16] Found samclip - /usr/local/bin/samclip [23:01:16] Found seqtk - /usr/local/bin/seqtk [23:01:16] Found parallel - /usr/local/bin/parallel [23:01:16] Found freebayes - /usr/local/bin/freebayes [23:01:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [23:01:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [23:01:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [23:01:16] Found vcfuniq - /usr/local/bin/vcfuniq [23:01:16] Found vcffirstheader - /usr/local/bin/vcffirstheader [23:01:16] Found gzip - /bin/gzip [23:01:16] Found vt - /usr/local/bin/vt [23:01:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [23:01:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [23:01:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [23:01:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [23:01:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [23:01:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [23:01:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [23:01:17] Please supply a reference FASTA/GBK/EMBL file with --reference
1[21:21:34] This is snippy 4.6.0
Show full stderr[21:21:34] This is snippy 4.6.0 [21:21:34] Written by Torsten Seemann [21:21:34] Obtained from https://github.com/tseemann/snippy [21:21:34] Detected operating system: linux [21:21:34] Enabling bundled linux tools. [21:21:34] Found bwa - /usr/local/bin/bwa [21:21:34] Found bcftools - /usr/local/bin/bcftools [21:21:34] Found samtools - /usr/local/bin/samtools [21:21:34] Found java - /usr/local/bin/java [21:21:34] Found snpEff - /usr/local/bin/snpEff [21:21:34] Found samclip - /usr/local/bin/samclip [21:21:34] Found seqtk - /usr/local/bin/seqtk [21:21:34] Found parallel - /usr/local/bin/parallel [21:21:34] Found freebayes - /usr/local/bin/freebayes [21:21:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:21:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:21:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:21:34] Found vcfuniq - /usr/local/bin/vcfuniq [21:21:34] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:21:34] Found gzip - /bin/gzip [21:21:34] Found vt - /usr/local/bin/vt [21:21:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:21:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:21:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:21:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:21:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:21:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:21:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:21:35] Please supply a reference FASTA/GBK/EMBL file with --reference
1[02:08:34] This is snippy 4.6.0
Show full stderr[02:08:34] This is snippy 4.6.0 [02:08:34] Written by Torsten Seemann [02:08:34] Obtained from https://github.com/tseemann/snippy [02:08:34] Detected operating system: linux [02:08:34] Enabling bundled linux tools. [02:08:34] Found bwa - /usr/local/bin/bwa [02:08:34] Found bcftools - /usr/local/bin/bcftools [02:08:34] Found samtools - /usr/local/bin/samtools [02:08:34] Found java - /usr/local/bin/java [02:08:34] Found snpEff - /usr/local/bin/snpEff [02:08:34] Found samclip - /usr/local/bin/samclip [02:08:34] Found seqtk - /usr/local/bin/seqtk [02:08:34] Found parallel - /usr/local/bin/parallel [02:08:34] Found freebayes - /usr/local/bin/freebayes [02:08:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [02:08:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [02:08:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [02:08:34] Found vcfuniq - /usr/local/bin/vcfuniq [02:08:34] Found vcffirstheader - /usr/local/bin/vcffirstheader [02:08:34] Found gzip - /bin/gzip [02:08:34] Found vt - /usr/local/bin/vt [02:08:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [02:08:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [02:08:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [02:08:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [02:08:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [02:08:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [02:08:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [02:08:35] Please supply a reference FASTA/GBK/EMBL file with --reference
1[02:09:19] This is snippy 4.6.0
Show full stderr[02:09:19] This is snippy 4.6.0 [02:09:19] Written by Torsten Seemann [02:09:19] Obtained from https://github.com/tseemann/snippy [02:09:19] Detected operating system: linux [02:09:19] Enabling bundled linux tools. [02:09:19] Found bwa - /usr/local/bin/bwa [02:09:19] Found bcftools - /usr/local/bin/bcftools [02:09:19] Found samtools - /usr/local/bin/samtools [02:09:19] Found java - /usr/local/bin/java [02:09:19] Found snpEff - /usr/local/bin/snpEff [02:09:19] Found samclip - /usr/local/bin/samclip [02:09:19] Found seqtk - /usr/local/bin/seqtk [02:09:19] Found parallel - /usr/local/bin/parallel [02:09:19] Found freebayes - /usr/local/bin/freebayes [02:09:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [02:09:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [02:09:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [02:09:19] Found vcfuniq - /usr/local/bin/vcfuniq [02:09:19] Found vcffirstheader - /usr/local/bin/vcffirstheader [02:09:19] Found gzip - /bin/gzip [02:09:19] Found vt - /usr/local/bin/vt [02:09:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [02:09:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [02:09:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [02:09:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [02:09:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [02:09:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [02:09:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [02:09:21] Please supply a reference FASTA/GBK/EMBL file with --reference
1[02:09:38] This is snippy 4.6.0
Show full stderr[02:09:38] This is snippy 4.6.0 [02:09:38] Written by Torsten Seemann [02:09:38] Obtained from https://github.com/tseemann/snippy [02:09:38] Detected operating system: linux [02:09:38] Enabling bundled linux tools. [02:09:38] Found bwa - /usr/local/bin/bwa [02:09:38] Found bcftools - /usr/local/bin/bcftools [02:09:38] Found samtools - /usr/local/bin/samtools [02:09:38] Found java - /usr/local/bin/java [02:09:38] Found snpEff - /usr/local/bin/snpEff [02:09:38] Found samclip - /usr/local/bin/samclip [02:09:38] Found seqtk - /usr/local/bin/seqtk [02:09:38] Found parallel - /usr/local/bin/parallel [02:09:38] Found freebayes - /usr/local/bin/freebayes [02:09:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [02:09:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [02:09:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [02:09:38] Found vcfuniq - /usr/local/bin/vcfuniq [02:09:38] Found vcffirstheader - /usr/local/bin/vcffirstheader [02:09:38] Found gzip - /bin/gzip [02:09:38] Found vt - /usr/local/bin/vt [02:09:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [02:09:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [02:09:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [02:09:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [02:09:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [02:09:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [02:09:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [02:09:39] Please supply a reference FASTA/GBK/EMBL file with --reference
1[21:20:39] This is snippy 4.6.0
Show full stderr[21:20:39] This is snippy 4.6.0 [21:20:39] Written by Torsten Seemann [21:20:39] Obtained from https://github.com/tseemann/snippy [21:20:39] Detected operating system: linux [21:20:39] Enabling bundled linux tools. [21:20:39] Found bwa - /usr/local/bin/bwa [21:20:39] Found bcftools - /usr/local/bin/bcftools [21:20:39] Found samtools - /usr/local/bin/samtools [21:20:39] Found java - /usr/local/bin/java [21:20:39] Found snpEff - /usr/local/bin/snpEff [21:20:39] Found samclip - /usr/local/bin/samclip [21:20:39] Found seqtk - /usr/local/bin/seqtk [21:20:39] Found parallel - /usr/local/bin/parallel [21:20:39] Found freebayes - /usr/local/bin/freebayes [21:20:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:20:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:20:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:20:39] Found vcfuniq - /usr/local/bin/vcfuniq [21:20:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:20:39] Found gzip - /bin/gzip [21:20:39] Found vt - /usr/local/bin/vt [21:20:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:20:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:20:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:20:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:20:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:20:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:20:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:20:40] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:42:26] This is snippy 4.6.0
Show full stderr[17:42:26] This is snippy 4.6.0 [17:42:26] Written by Torsten Seemann [17:42:26] Obtained from https://github.com/tseemann/snippy [17:42:26] Detected operating system: linux [17:42:26] Enabling bundled linux tools. [17:42:26] Found bwa - /usr/local/bin/bwa [17:42:26] Found bcftools - /usr/local/bin/bcftools [17:42:26] Found samtools - /usr/local/bin/samtools [17:42:26] Found java - /usr/local/bin/java [17:42:26] Found snpEff - /usr/local/bin/snpEff [17:42:26] Found samclip - /usr/local/bin/samclip [17:42:26] Found seqtk - /usr/local/bin/seqtk [17:42:26] Found parallel - /usr/local/bin/parallel [17:42:26] Found freebayes - /usr/local/bin/freebayes [17:42:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:42:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:42:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:42:26] Found vcfuniq - /usr/local/bin/vcfuniq [17:42:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:42:27] Found gzip - /bin/gzip [17:42:27] Found vt - /usr/local/bin/vt [17:42:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:42:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:42:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:42:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:42:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:42:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:42:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:42:27] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:09:47] This is snippy 4.6.0
Show full stderr[01:09:47] This is snippy 4.6.0 [01:09:47] Written by Torsten Seemann [01:09:47] Obtained from https://github.com/tseemann/snippy [01:09:47] Detected operating system: linux [01:09:47] Enabling bundled linux tools. [01:09:47] Found bwa - /usr/local/bin/bwa [01:09:47] Found bcftools - /usr/local/bin/bcftools [01:09:47] Found samtools - /usr/local/bin/samtools [01:09:47] Found java - /usr/local/bin/java [01:09:47] Found snpEff - /usr/local/bin/snpEff [01:09:47] Found samclip - /usr/local/bin/samclip [01:09:47] Found seqtk - /usr/local/bin/seqtk [01:09:47] Found parallel - /usr/local/bin/parallel [01:09:47] Found freebayes - /usr/local/bin/freebayes [01:09:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:09:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:09:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:09:47] Found vcfuniq - /usr/local/bin/vcfuniq [01:09:47] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:09:47] Found gzip - /bin/gzip [01:09:47] Found vt - /usr/local/bin/vt [01:09:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:09:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:09:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:09:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:09:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:09:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:09:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:09:48] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:18:17] This is snippy 4.6.0
Show full stderr[01:18:17] This is snippy 4.6.0 [01:18:17] Written by Torsten Seemann [01:18:17] Obtained from https://github.com/tseemann/snippy [01:18:17] Detected operating system: linux [01:18:17] Enabling bundled linux tools. [01:18:17] Found bwa - /usr/local/bin/bwa [01:18:17] Found bcftools - /usr/local/bin/bcftools [01:18:17] Found samtools - /usr/local/bin/samtools [01:18:17] Found java - /usr/local/bin/java [01:18:17] Found snpEff - /usr/local/bin/snpEff [01:18:17] Found samclip - /usr/local/bin/samclip [01:18:17] Found seqtk - /usr/local/bin/seqtk [01:18:17] Found parallel - /usr/local/bin/parallel [01:18:17] Found freebayes - /usr/local/bin/freebayes [01:18:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:18:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:18:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:18:17] Found vcfuniq - /usr/local/bin/vcfuniq [01:18:17] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:18:17] Found gzip - /bin/gzip [01:18:17] Found vt - /usr/local/bin/vt [01:18:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:18:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:18:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:18:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:18:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:18:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:18:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:18:18] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:25:58] This is snippy 4.6.0
Show full stderr[01:25:58] This is snippy 4.6.0 [01:25:58] Written by Torsten Seemann [01:25:58] Obtained from https://github.com/tseemann/snippy [01:25:58] Detected operating system: linux [01:25:58] Enabling bundled linux tools. [01:25:58] Found bwa - /usr/local/bin/bwa [01:25:58] Found bcftools - /usr/local/bin/bcftools [01:25:58] Found samtools - /usr/local/bin/samtools [01:25:58] Found java - /usr/local/bin/java [01:25:58] Found snpEff - /usr/local/bin/snpEff [01:25:58] Found samclip - /usr/local/bin/samclip [01:25:58] Found seqtk - /usr/local/bin/seqtk [01:25:58] Found parallel - /usr/local/bin/parallel [01:25:58] Found freebayes - /usr/local/bin/freebayes [01:25:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:25:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:25:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:25:58] Found vcfuniq - /usr/local/bin/vcfuniq [01:25:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:25:58] Found gzip - /bin/gzip [01:25:58] Found vt - /usr/local/bin/vt [01:25:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:25:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:25:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:25:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:25:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:25:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:25:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:25:59] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:26:13] This is snippy 4.6.0
Show full stderr[01:26:13] This is snippy 4.6.0 [01:26:13] Written by Torsten Seemann [01:26:13] Obtained from https://github.com/tseemann/snippy [01:26:13] Detected operating system: linux [01:26:13] Enabling bundled linux tools. [01:26:13] Found bwa - /usr/local/bin/bwa [01:26:13] Found bcftools - /usr/local/bin/bcftools [01:26:13] Found samtools - /usr/local/bin/samtools [01:26:13] Found java - /usr/local/bin/java [01:26:13] Found snpEff - /usr/local/bin/snpEff [01:26:13] Found samclip - /usr/local/bin/samclip [01:26:13] Found seqtk - /usr/local/bin/seqtk [01:26:13] Found parallel - /usr/local/bin/parallel [01:26:13] Found freebayes - /usr/local/bin/freebayes [01:26:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:26:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:26:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:26:13] Found vcfuniq - /usr/local/bin/vcfuniq [01:26:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:26:13] Found gzip - /bin/gzip [01:26:13] Found vt - /usr/local/bin/vt [01:26:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:26:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:26:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:26:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:26:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:26:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:26:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:26:14] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:35:17] This is snippy 4.6.0
Show full stderr[01:35:17] This is snippy 4.6.0 [01:35:17] Written by Torsten Seemann [01:35:17] Obtained from https://github.com/tseemann/snippy [01:35:17] Detected operating system: linux [01:35:17] Enabling bundled linux tools. [01:35:17] Found bwa - /usr/local/bin/bwa [01:35:17] Found bcftools - /usr/local/bin/bcftools [01:35:17] Found samtools - /usr/local/bin/samtools [01:35:17] Found java - /usr/local/bin/java [01:35:17] Found snpEff - /usr/local/bin/snpEff [01:35:17] Found samclip - /usr/local/bin/samclip [01:35:17] Found seqtk - /usr/local/bin/seqtk [01:35:18] Found parallel - /usr/local/bin/parallel [01:35:18] Found freebayes - /usr/local/bin/freebayes [01:35:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:35:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:35:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:35:18] Found vcfuniq - /usr/local/bin/vcfuniq [01:35:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:35:18] Found gzip - /bin/gzip [01:35:18] Found vt - /usr/local/bin/vt [01:35:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:35:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:35:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:35:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:35:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:35:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:35:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:35:18] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:50:59] This is snippy 4.6.0
Show full stderr[01:50:59] This is snippy 4.6.0 [01:50:59] Written by Torsten Seemann [01:50:59] Obtained from https://github.com/tseemann/snippy [01:50:59] Detected operating system: linux [01:50:59] Enabling bundled linux tools. [01:50:59] Found bwa - /usr/local/bin/bwa [01:51:00] Found bcftools - /usr/local/bin/bcftools [01:51:00] Found samtools - /usr/local/bin/samtools [01:51:00] Found java - /usr/local/bin/java [01:51:00] Found snpEff - /usr/local/bin/snpEff [01:51:00] Found samclip - /usr/local/bin/samclip [01:51:00] Found seqtk - /usr/local/bin/seqtk [01:51:00] Found parallel - /usr/local/bin/parallel [01:51:00] Found freebayes - /usr/local/bin/freebayes [01:51:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:51:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:51:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:51:00] Found vcfuniq - /usr/local/bin/vcfuniq [01:51:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:51:00] Found gzip - /bin/gzip [01:51:00] Found vt - /usr/local/bin/vt [01:51:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:51:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:51:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:51:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:51:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:51:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:51:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:51:01] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:51:16] This is snippy 4.6.0
Show full stderr[01:51:16] This is snippy 4.6.0 [01:51:16] Written by Torsten Seemann [01:51:16] Obtained from https://github.com/tseemann/snippy [01:51:16] Detected operating system: linux [01:51:16] Enabling bundled linux tools. [01:51:16] Found bwa - /usr/local/bin/bwa [01:51:16] Found bcftools - /usr/local/bin/bcftools [01:51:16] Found samtools - /usr/local/bin/samtools [01:51:16] Found java - /usr/local/bin/java [01:51:16] Found snpEff - /usr/local/bin/snpEff [01:51:16] Found samclip - /usr/local/bin/samclip [01:51:16] Found seqtk - /usr/local/bin/seqtk [01:51:16] Found parallel - /usr/local/bin/parallel [01:51:16] Found freebayes - /usr/local/bin/freebayes [01:51:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:51:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:51:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:51:16] Found vcfuniq - /usr/local/bin/vcfuniq [01:51:16] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:51:16] Found gzip - /bin/gzip [01:51:16] Found vt - /usr/local/bin/vt [01:51:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:51:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:51:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:51:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:51:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:51:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:51:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:51:17] Please supply a reference FASTA/GBK/EMBL file with --reference
1[20:05:50] This is snippy 4.6.0
Show full stderr[20:05:50] This is snippy 4.6.0 [20:05:50] Written by Torsten Seemann [20:05:50] Obtained from https://github.com/tseemann/snippy [20:05:50] Detected operating system: linux [20:05:50] Enabling bundled linux tools. [20:05:50] Found bwa - /usr/local/bin/bwa [20:05:50] Found bcftools - /usr/local/bin/bcftools [20:05:50] Found samtools - /usr/local/bin/samtools [20:05:50] Found java - /usr/local/bin/java [20:05:50] Found snpEff - /usr/local/bin/snpEff [20:05:50] Found samclip - /usr/local/bin/samclip [20:05:50] Found seqtk - /usr/local/bin/seqtk [20:05:50] Found parallel - /usr/local/bin/parallel [20:05:50] Found freebayes - /usr/local/bin/freebayes [20:05:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [20:05:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [20:05:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [20:05:50] Found vcfuniq - /usr/local/bin/vcfuniq [20:05:50] Found vcffirstheader - /usr/local/bin/vcffirstheader [20:05:50] Found gzip - /bin/gzip [20:05:50] Found vt - /usr/local/bin/vt [20:05:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [20:05:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [20:05:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [20:05:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [20:05:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [20:05:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [20:05:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [20:05:56] Please supply a reference FASTA/GBK/EMBL file with --reference
1[02:08:50] This is snippy 4.6.0
Show full stderr[02:08:50] This is snippy 4.6.0 [02:08:50] Written by Torsten Seemann [02:08:50] Obtained from https://github.com/tseemann/snippy [02:08:50] Detected operating system: linux [02:08:50] Enabling bundled linux tools. [02:08:50] Found bwa - /usr/local/bin/bwa [02:08:50] Found bcftools - /usr/local/bin/bcftools [02:08:50] Found samtools - /usr/local/bin/samtools [02:08:50] Found java - /usr/local/bin/java [02:08:50] Found snpEff - /usr/local/bin/snpEff [02:08:50] Found samclip - /usr/local/bin/samclip [02:08:50] Found seqtk - /usr/local/bin/seqtk [02:08:50] Found parallel - /usr/local/bin/parallel [02:08:50] Found freebayes - /usr/local/bin/freebayes [02:08:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [02:08:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [02:08:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [02:08:50] Found vcfuniq - /usr/local/bin/vcfuniq [02:08:50] Found vcffirstheader - /usr/local/bin/vcffirstheader [02:08:50] Found gzip - /bin/gzip [02:08:50] Found vt - /usr/local/bin/vt [02:08:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [02:08:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [02:08:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [02:08:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [02:08:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [02:08:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [02:08:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [02:08:51] Please supply a reference FASTA/GBK/EMBL file with --reference
1[02:09:04] This is snippy 4.6.0
Show full stderr[02:09:04] This is snippy 4.6.0 [02:09:04] Written by Torsten Seemann [02:09:04] Obtained from https://github.com/tseemann/snippy [02:09:04] Detected operating system: linux [02:09:04] Enabling bundled linux tools. [02:09:04] Found bwa - /usr/local/bin/bwa [02:09:04] Found bcftools - /usr/local/bin/bcftools [02:09:04] Found samtools - /usr/local/bin/samtools [02:09:04] Found java - /usr/local/bin/java [02:09:04] Found snpEff - /usr/local/bin/snpEff [02:09:04] Found samclip - /usr/local/bin/samclip [02:09:04] Found seqtk - /usr/local/bin/seqtk [02:09:04] Found parallel - /usr/local/bin/parallel [02:09:04] Found freebayes - /usr/local/bin/freebayes [02:09:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [02:09:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [02:09:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [02:09:04] Found vcfuniq - /usr/local/bin/vcfuniq [02:09:04] Found vcffirstheader - /usr/local/bin/vcffirstheader [02:09:04] Found gzip - /bin/gzip [02:09:04] Found vt - /usr/local/bin/vt [02:09:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [02:09:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [02:09:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [02:09:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [02:09:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [02:09:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [02:09:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [02:09:05] Please supply a reference FASTA/GBK/EMBL file with --reference
1[02:09:54] This is snippy 4.6.0
Show full stderr[02:09:54] This is snippy 4.6.0 [02:09:54] Written by Torsten Seemann [02:09:54] Obtained from https://github.com/tseemann/snippy [02:09:54] Detected operating system: linux [02:09:54] Enabling bundled linux tools. [02:09:54] Found bwa - /usr/local/bin/bwa [02:09:54] Found bcftools - /usr/local/bin/bcftools [02:09:54] Found samtools - /usr/local/bin/samtools [02:09:54] Found java - /usr/local/bin/java [02:09:54] Found snpEff - /usr/local/bin/snpEff [02:09:54] Found samclip - /usr/local/bin/samclip [02:09:54] Found seqtk - /usr/local/bin/seqtk [02:09:54] Found parallel - /usr/local/bin/parallel [02:09:54] Found freebayes - /usr/local/bin/freebayes [02:09:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [02:09:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [02:09:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [02:09:54] Found vcfuniq - /usr/local/bin/vcfuniq [02:09:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [02:09:54] Found gzip - /bin/gzip [02:09:54] Found vt - /usr/local/bin/vt [02:09:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [02:09:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [02:09:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [02:09:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [02:09:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [02:09:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [02:09:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [02:09:55] Please supply a reference FASTA/GBK/EMBL file with --reference
1[02:10:17] This is snippy 4.6.0
Show full stderr[02:10:17] This is snippy 4.6.0 [02:10:17] Written by Torsten Seemann [02:10:17] Obtained from https://github.com/tseemann/snippy [02:10:17] Detected operating system: linux [02:10:17] Enabling bundled linux tools. [02:10:17] Found bwa - /usr/local/bin/bwa [02:10:17] Found bcftools - /usr/local/bin/bcftools [02:10:17] Found samtools - /usr/local/bin/samtools [02:10:17] Found java - /usr/local/bin/java [02:10:18] Found snpEff - /usr/local/bin/snpEff [02:10:18] Found samclip - /usr/local/bin/samclip [02:10:18] Found seqtk - /usr/local/bin/seqtk [02:10:18] Found parallel - /usr/local/bin/parallel [02:10:18] Found freebayes - /usr/local/bin/freebayes [02:10:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [02:10:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [02:10:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [02:10:18] Found vcfuniq - /usr/local/bin/vcfuniq [02:10:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [02:10:18] Found gzip - /bin/gzip [02:10:18] Found vt - /usr/local/bin/vt [02:10:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [02:10:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [02:10:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [02:10:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [02:10:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [02:10:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [02:10:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [02:10:18] Please supply a reference FASTA/GBK/EMBL file with --reference
1[02:17:59] This is snippy 4.6.0
Show full stderr[02:17:59] This is snippy 4.6.0 [02:17:59] Written by Torsten Seemann [02:17:59] Obtained from https://github.com/tseemann/snippy [02:17:59] Detected operating system: linux [02:17:59] Enabling bundled linux tools. [02:17:59] Found bwa - /usr/local/bin/bwa [02:17:59] Found bcftools - /usr/local/bin/bcftools [02:17:59] Found samtools - /usr/local/bin/samtools [02:17:59] Found java - /usr/local/bin/java [02:17:59] Found snpEff - /usr/local/bin/snpEff [02:17:59] Found samclip - /usr/local/bin/samclip [02:17:59] Found seqtk - /usr/local/bin/seqtk [02:17:59] Found parallel - /usr/local/bin/parallel [02:17:59] Found freebayes - /usr/local/bin/freebayes [02:17:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [02:17:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [02:17:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [02:17:59] Found vcfuniq - /usr/local/bin/vcfuniq [02:17:59] Found vcffirstheader - /usr/local/bin/vcffirstheader [02:17:59] Found gzip - /bin/gzip [02:17:59] Found vt - /usr/local/bin/vt [02:17:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [02:17:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [02:18:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [02:18:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [02:18:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [02:18:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [02:18:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [02:18:00] Please supply a reference FASTA/GBK/EMBL file with --reference
1[02:18:13] This is snippy 4.6.0
Show full stderr[02:18:13] This is snippy 4.6.0 [02:18:13] Written by Torsten Seemann [02:18:13] Obtained from https://github.com/tseemann/snippy [02:18:13] Detected operating system: linux [02:18:13] Enabling bundled linux tools. [02:18:13] Found bwa - /usr/local/bin/bwa [02:18:13] Found bcftools - /usr/local/bin/bcftools [02:18:13] Found samtools - /usr/local/bin/samtools [02:18:13] Found java - /usr/local/bin/java [02:18:13] Found snpEff - /usr/local/bin/snpEff [02:18:13] Found samclip - /usr/local/bin/samclip [02:18:13] Found seqtk - /usr/local/bin/seqtk [02:18:13] Found parallel - /usr/local/bin/parallel [02:18:13] Found freebayes - /usr/local/bin/freebayes [02:18:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [02:18:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [02:18:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [02:18:13] Found vcfuniq - /usr/local/bin/vcfuniq [02:18:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [02:18:13] Found gzip - /bin/gzip [02:18:13] Found vt - /usr/local/bin/vt [02:18:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [02:18:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [02:18:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [02:18:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [02:18:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [02:18:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [02:18:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [02:18:15] Please supply a reference FASTA/GBK/EMBL file with --reference
1[02:18:29] This is snippy 4.6.0
Show full stderr[02:18:29] This is snippy 4.6.0 [02:18:29] Written by Torsten Seemann [02:18:29] Obtained from https://github.com/tseemann/snippy [02:18:29] Detected operating system: linux [02:18:29] Enabling bundled linux tools. [02:18:29] Found bwa - /usr/local/bin/bwa [02:18:29] Found bcftools - /usr/local/bin/bcftools [02:18:29] Found samtools - /usr/local/bin/samtools [02:18:29] Found java - /usr/local/bin/java [02:18:29] Found snpEff - /usr/local/bin/snpEff [02:18:29] Found samclip - /usr/local/bin/samclip [02:18:29] Found seqtk - /usr/local/bin/seqtk [02:18:29] Found parallel - /usr/local/bin/parallel [02:18:29] Found freebayes - /usr/local/bin/freebayes [02:18:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [02:18:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [02:18:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [02:18:29] Found vcfuniq - /usr/local/bin/vcfuniq [02:18:29] Found vcffirstheader - /usr/local/bin/vcffirstheader [02:18:29] Found gzip - /bin/gzip [02:18:29] Found vt - /usr/local/bin/vt [02:18:29] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [02:18:29] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [02:18:29] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [02:18:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [02:18:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [02:18:30] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [02:18:30] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [02:18:30] Please supply a reference FASTA/GBK/EMBL file with --reference
1[23:02:18] This is snippy 4.6.0
Show full stderr[23:02:18] This is snippy 4.6.0 [23:02:18] Written by Torsten Seemann [23:02:18] Obtained from https://github.com/tseemann/snippy [23:02:18] Detected operating system: linux [23:02:18] Enabling bundled linux tools. [23:02:18] Found bwa - /usr/local/bin/bwa [23:02:18] Found bcftools - /usr/local/bin/bcftools [23:02:18] Found samtools - /usr/local/bin/samtools [23:02:18] Found java - /usr/local/bin/java [23:02:18] Found snpEff - /usr/local/bin/snpEff [23:02:18] Found samclip - /usr/local/bin/samclip [23:02:18] Found seqtk - /usr/local/bin/seqtk [23:02:18] Found parallel - /usr/local/bin/parallel [23:02:18] Found freebayes - /usr/local/bin/freebayes [23:02:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [23:02:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [23:02:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [23:02:18] Found vcfuniq - /usr/local/bin/vcfuniq [23:02:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [23:02:18] Found gzip - /bin/gzip [23:02:18] Found vt - /usr/local/bin/vt [23:02:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [23:02:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [23:02:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [23:02:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [23:02:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [23:02:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [23:02:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [23:02:18] Please supply a reference FASTA/GBK/EMBL file with --reference
1[23:26:27] This is snippy 4.6.0
Show full stderr[23:26:27] This is snippy 4.6.0 [23:26:27] Written by Torsten Seemann [23:26:27] Obtained from https://github.com/tseemann/snippy [23:26:27] Detected operating system: linux [23:26:27] Enabling bundled linux tools. [23:26:27] Found bwa - /usr/local/bin/bwa [23:26:27] Found bcftools - /usr/local/bin/bcftools [23:26:27] Found samtools - /usr/local/bin/samtools [23:26:27] Found java - /usr/local/bin/java [23:26:27] Found snpEff - /usr/local/bin/snpEff [23:26:27] Found samclip - /usr/local/bin/samclip [23:26:27] Found seqtk - /usr/local/bin/seqtk [23:26:27] Found parallel - /usr/local/bin/parallel [23:26:27] Found freebayes - /usr/local/bin/freebayes [23:26:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [23:26:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [23:26:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [23:26:27] Found vcfuniq - /usr/local/bin/vcfuniq [23:26:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [23:26:27] Found gzip - /bin/gzip [23:26:27] Found vt - /usr/local/bin/vt [23:26:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [23:26:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [23:26:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [23:26:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [23:26:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [23:26:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [23:26:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [23:26:28] Please supply a reference FASTA/GBK/EMBL file with --reference
1[23:27:06] This is snippy 4.6.0
Show full stderr[23:27:06] This is snippy 4.6.0 [23:27:06] Written by Torsten Seemann [23:27:06] Obtained from https://github.com/tseemann/snippy [23:27:06] Detected operating system: linux [23:27:06] Enabling bundled linux tools. [23:27:06] Found bwa - /usr/local/bin/bwa [23:27:06] Found bcftools - /usr/local/bin/bcftools [23:27:06] Found samtools - /usr/local/bin/samtools [23:27:06] Found java - /usr/local/bin/java [23:27:06] Found snpEff - /usr/local/bin/snpEff [23:27:06] Found samclip - /usr/local/bin/samclip [23:27:06] Found seqtk - /usr/local/bin/seqtk [23:27:06] Found parallel - /usr/local/bin/parallel [23:27:06] Found freebayes - /usr/local/bin/freebayes [23:27:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [23:27:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [23:27:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [23:27:06] Found vcfuniq - /usr/local/bin/vcfuniq [23:27:06] Found vcffirstheader - /usr/local/bin/vcffirstheader [23:27:06] Found gzip - /bin/gzip [23:27:06] Found vt - /usr/local/bin/vt [23:27:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [23:27:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [23:27:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [23:27:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [23:27:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [23:27:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [23:27:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [23:27:07] Please supply a reference FASTA/GBK/EMBL file with --reference
1[23:42:44] This is snippy 4.6.0
Show full stderr[23:42:44] This is snippy 4.6.0 [23:42:44] Written by Torsten Seemann [23:42:44] Obtained from https://github.com/tseemann/snippy [23:42:44] Detected operating system: linux [23:42:44] Enabling bundled linux tools. [23:42:44] Found bwa - /usr/local/bin/bwa [23:42:44] Found bcftools - /usr/local/bin/bcftools [23:42:44] Found samtools - /usr/local/bin/samtools [23:42:44] Found java - /usr/local/bin/java [23:42:44] Found snpEff - /usr/local/bin/snpEff [23:42:44] Found samclip - /usr/local/bin/samclip [23:42:44] Found seqtk - /usr/local/bin/seqtk [23:42:44] Found parallel - /usr/local/bin/parallel [23:42:44] Found freebayes - /usr/local/bin/freebayes [23:42:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [23:42:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [23:42:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [23:42:44] Found vcfuniq - /usr/local/bin/vcfuniq [23:42:44] Found vcffirstheader - /usr/local/bin/vcffirstheader [23:42:44] Found gzip - /bin/gzip [23:42:44] Found vt - /usr/local/bin/vt [23:42:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [23:42:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [23:42:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [23:42:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [23:42:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [23:42:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [23:42:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [23:42:45] Please supply a reference FASTA/GBK/EMBL file with --reference
1[23:43:06] This is snippy 4.6.0
Show full stderr[23:43:06] This is snippy 4.6.0 [23:43:06] Written by Torsten Seemann [23:43:06] Obtained from https://github.com/tseemann/snippy [23:43:06] Detected operating system: linux [23:43:06] Enabling bundled linux tools. [23:43:06] Found bwa - /usr/local/bin/bwa [23:43:06] Found bcftools - /usr/local/bin/bcftools [23:43:06] Found samtools - /usr/local/bin/samtools [23:43:06] Found java - /usr/local/bin/java [23:43:06] Found snpEff - /usr/local/bin/snpEff [23:43:06] Found samclip - /usr/local/bin/samclip [23:43:06] Found seqtk - /usr/local/bin/seqtk [23:43:06] Found parallel - /usr/local/bin/parallel [23:43:06] Found freebayes - /usr/local/bin/freebayes [23:43:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [23:43:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [23:43:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [23:43:06] Found vcfuniq - /usr/local/bin/vcfuniq [23:43:06] Found vcffirstheader - /usr/local/bin/vcffirstheader [23:43:06] Found gzip - /bin/gzip [23:43:06] Found vt - /usr/local/bin/vt [23:43:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [23:43:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [23:43:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [23:43:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [23:43:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [23:43:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [23:43:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [23:43:06] Please supply a reference FASTA/GBK/EMBL file with --reference
1[23:59:12] This is snippy 4.6.0
Show full stderr[23:59:12] This is snippy 4.6.0 [23:59:12] Written by Torsten Seemann [23:59:12] Obtained from https://github.com/tseemann/snippy [23:59:12] Detected operating system: linux [23:59:12] Enabling bundled linux tools. [23:59:12] Found bwa - /usr/local/bin/bwa [23:59:12] Found bcftools - /usr/local/bin/bcftools [23:59:12] Found samtools - /usr/local/bin/samtools [23:59:12] Found java - /usr/local/bin/java [23:59:12] Found snpEff - /usr/local/bin/snpEff [23:59:12] Found samclip - /usr/local/bin/samclip [23:59:12] Found seqtk - /usr/local/bin/seqtk [23:59:12] Found parallel - /usr/local/bin/parallel [23:59:12] Found freebayes - /usr/local/bin/freebayes [23:59:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [23:59:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [23:59:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [23:59:12] Found vcfuniq - /usr/local/bin/vcfuniq [23:59:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [23:59:12] Found gzip - /bin/gzip [23:59:12] Found vt - /usr/local/bin/vt [23:59:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [23:59:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [23:59:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [23:59:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [23:59:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [23:59:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [23:59:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [23:59:13] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:52:58] This is snippy 4.6.0
Show full stderr[17:52:58] This is snippy 4.6.0 [17:52:58] Written by Torsten Seemann [17:52:58] Obtained from https://github.com/tseemann/snippy [17:52:58] Detected operating system: linux [17:52:58] Enabling bundled linux tools. [17:52:58] Found bwa - /usr/local/bin/bwa [17:52:58] Found bcftools - /usr/local/bin/bcftools [17:52:58] Found samtools - /usr/local/bin/samtools [17:52:58] Found java - /usr/local/bin/java [17:52:58] Found snpEff - /usr/local/bin/snpEff [17:52:58] Found samclip - /usr/local/bin/samclip [17:52:58] Found seqtk - /usr/local/bin/seqtk [17:52:58] Found parallel - /usr/local/bin/parallel [17:52:58] Found freebayes - /usr/local/bin/freebayes [17:52:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:52:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:52:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:52:58] Found vcfuniq - /usr/local/bin/vcfuniq [17:52:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:52:58] Found gzip - /bin/gzip [17:52:58] Found vt - /usr/local/bin/vt [17:52:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:52:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:52:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:52:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:52:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:52:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:52:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:52:59] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:07:28] This is snippy 4.6.0
Show full stderr[00:07:28] This is snippy 4.6.0 [00:07:28] Written by Torsten Seemann [00:07:28] Obtained from https://github.com/tseemann/snippy [00:07:28] Detected operating system: linux [00:07:28] Enabling bundled linux tools. [00:07:28] Found bwa - /usr/local/bin/bwa [00:07:28] Found bcftools - /usr/local/bin/bcftools [00:07:29] Found samtools - /usr/local/bin/samtools [00:07:29] Found java - /usr/local/bin/java [00:07:29] Found snpEff - /usr/local/bin/snpEff [00:07:29] Found samclip - /usr/local/bin/samclip [00:07:29] Found seqtk - /usr/local/bin/seqtk [00:07:29] Found parallel - /usr/local/bin/parallel [00:07:29] Found freebayes - /usr/local/bin/freebayes [00:07:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:07:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:07:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:07:29] Found vcfuniq - /usr/local/bin/vcfuniq [00:07:29] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:07:29] Found gzip - /bin/gzip [00:07:29] Found vt - /usr/local/bin/vt [00:07:29] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:07:29] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:07:29] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:07:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:07:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:07:30] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:07:30] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:07:30] Please supply a reference FASTA/GBK/EMBL file with --reference
1[18:09:26] This is snippy 4.6.0
Show full stderr[18:09:26] This is snippy 4.6.0 [18:09:26] Written by Torsten Seemann [18:09:26] Obtained from https://github.com/tseemann/snippy [18:09:26] Detected operating system: linux [18:09:26] Enabling bundled linux tools. [18:09:26] Found bwa - /usr/local/bin/bwa [18:09:26] Found bcftools - /usr/local/bin/bcftools [18:09:26] Found samtools - /usr/local/bin/samtools [18:09:26] Found java - /usr/local/bin/java [18:09:26] Found snpEff - /usr/local/bin/snpEff [18:09:26] Found samclip - /usr/local/bin/samclip [18:09:26] Found seqtk - /usr/local/bin/seqtk [18:09:26] Found parallel - /usr/local/bin/parallel [18:09:26] Found freebayes - /usr/local/bin/freebayes [18:09:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [18:09:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [18:09:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [18:09:26] Found vcfuniq - /usr/local/bin/vcfuniq [18:09:26] Found vcffirstheader - /usr/local/bin/vcffirstheader [18:09:26] Found gzip - /bin/gzip [18:09:26] Found vt - /usr/local/bin/vt [18:09:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [18:09:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [18:09:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [18:09:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [18:09:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [18:09:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [18:09:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [18:09:27] Please supply a reference FASTA/GBK/EMBL file with --reference
1[22:03:19] This is snippy 4.6.0
Show full stderr[22:03:19] This is snippy 4.6.0 [22:03:19] Written by Torsten Seemann [22:03:19] Obtained from https://github.com/tseemann/snippy [22:03:19] Detected operating system: linux [22:03:19] Enabling bundled linux tools. [22:03:19] Found bwa - /usr/local/bin/bwa [22:03:19] Found bcftools - /usr/local/bin/bcftools [22:03:19] Found samtools - /usr/local/bin/samtools [22:03:19] Found java - /usr/local/bin/java [22:03:19] Found snpEff - /usr/local/bin/snpEff [22:03:19] Found samclip - /usr/local/bin/samclip [22:03:19] Found seqtk - /usr/local/bin/seqtk [22:03:19] Found parallel - /usr/local/bin/parallel [22:03:19] Found freebayes - /usr/local/bin/freebayes [22:03:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [22:03:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [22:03:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [22:03:19] Found vcfuniq - /usr/local/bin/vcfuniq [22:03:19] Found vcffirstheader - /usr/local/bin/vcffirstheader [22:03:19] Found gzip - /bin/gzip [22:03:19] Found vt - /usr/local/bin/vt [22:03:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [22:03:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [22:03:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [22:03:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [22:03:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [22:03:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [22:03:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [22:03:20] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:17:06] This is snippy 4.6.0
Show full stderr[00:17:06] This is snippy 4.6.0 [00:17:06] Written by Torsten Seemann [00:17:06] Obtained from https://github.com/tseemann/snippy [00:17:06] Detected operating system: linux [00:17:06] Enabling bundled linux tools. [00:17:06] Found bwa - /usr/local/bin/bwa [00:17:06] Found bcftools - /usr/local/bin/bcftools [00:17:06] Found samtools - /usr/local/bin/samtools [00:17:06] Found java - /usr/local/bin/java [00:17:06] Found snpEff - /usr/local/bin/snpEff [00:17:06] Found samclip - /usr/local/bin/samclip [00:17:06] Found seqtk - /usr/local/bin/seqtk [00:17:06] Found parallel - /usr/local/bin/parallel [00:17:06] Found freebayes - /usr/local/bin/freebayes [00:17:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:17:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:17:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:17:06] Found vcfuniq - /usr/local/bin/vcfuniq [00:17:06] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:17:06] Found gzip - /bin/gzip [00:17:06] Found vt - /usr/local/bin/vt [00:17:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:17:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:17:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:17:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:17:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:17:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:17:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:17:07] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:43:37] This is snippy 4.6.0
Show full stderr[00:43:37] This is snippy 4.6.0 [00:43:37] Written by Torsten Seemann [00:43:37] Obtained from https://github.com/tseemann/snippy [00:43:37] Detected operating system: linux [00:43:37] Enabling bundled linux tools. [00:43:37] Found bwa - /usr/local/bin/bwa [00:43:37] Found bcftools - /usr/local/bin/bcftools [00:43:37] Found samtools - /usr/local/bin/samtools [00:43:37] Found java - /usr/local/bin/java [00:43:37] Found snpEff - /usr/local/bin/snpEff [00:43:37] Found samclip - /usr/local/bin/samclip [00:43:37] Found seqtk - /usr/local/bin/seqtk [00:43:37] Found parallel - /usr/local/bin/parallel [00:43:37] Found freebayes - /usr/local/bin/freebayes [00:43:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:43:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:43:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:43:37] Found vcfuniq - /usr/local/bin/vcfuniq [00:43:37] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:43:37] Found gzip - /bin/gzip [00:43:37] Found vt - /usr/local/bin/vt [00:43:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:43:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:43:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:43:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:43:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:43:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:43:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:43:38] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:44:33] This is snippy 4.6.0
Show full stderr[00:44:33] This is snippy 4.6.0 [00:44:33] Written by Torsten Seemann [00:44:33] Obtained from https://github.com/tseemann/snippy [00:44:33] Detected operating system: linux [00:44:33] Enabling bundled linux tools. [00:44:33] Found bwa - /usr/local/bin/bwa [00:44:33] Found bcftools - /usr/local/bin/bcftools [00:44:33] Found samtools - /usr/local/bin/samtools [00:44:33] Found java - /usr/local/bin/java [00:44:33] Found snpEff - /usr/local/bin/snpEff [00:44:33] Found samclip - /usr/local/bin/samclip [00:44:33] Found seqtk - /usr/local/bin/seqtk [00:44:33] Found parallel - /usr/local/bin/parallel [00:44:33] Found freebayes - /usr/local/bin/freebayes [00:44:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:44:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:44:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:44:33] Found vcfuniq - /usr/local/bin/vcfuniq [00:44:33] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:44:33] Found gzip - /bin/gzip [00:44:33] Found vt - /usr/local/bin/vt [00:44:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:44:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:44:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:44:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:44:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:44:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:44:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:44:34] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:17:27] This is snippy 4.6.0
Show full stderr[01:17:27] This is snippy 4.6.0 [01:17:27] Written by Torsten Seemann [01:17:27] Obtained from https://github.com/tseemann/snippy [01:17:27] Detected operating system: linux [01:17:27] Enabling bundled linux tools. [01:17:27] Found bwa - /usr/local/bin/bwa [01:17:27] Found bcftools - /usr/local/bin/bcftools [01:17:27] Found samtools - /usr/local/bin/samtools [01:17:27] Found java - /usr/local/bin/java [01:17:27] Found snpEff - /usr/local/bin/snpEff [01:17:27] Found samclip - /usr/local/bin/samclip [01:17:27] Found seqtk - /usr/local/bin/seqtk [01:17:27] Found parallel - /usr/local/bin/parallel [01:17:27] Found freebayes - /usr/local/bin/freebayes [01:17:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:17:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:17:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:17:27] Found vcfuniq - /usr/local/bin/vcfuniq [01:17:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:17:27] Found gzip - /bin/gzip [01:17:27] Found vt - /usr/local/bin/vt [01:17:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:17:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:17:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:17:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:17:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:17:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:17:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:17:28] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:17:55] This is snippy 4.6.0
Show full stderr[01:17:55] This is snippy 4.6.0 [01:17:55] Written by Torsten Seemann [01:17:55] Obtained from https://github.com/tseemann/snippy [01:17:55] Detected operating system: linux [01:17:55] Enabling bundled linux tools. [01:17:55] Found bwa - /usr/local/bin/bwa [01:17:55] Found bcftools - /usr/local/bin/bcftools [01:17:55] Found samtools - /usr/local/bin/samtools [01:17:55] Found java - /usr/local/bin/java [01:17:55] Found snpEff - /usr/local/bin/snpEff [01:17:55] Found samclip - /usr/local/bin/samclip [01:17:55] Found seqtk - /usr/local/bin/seqtk [01:17:55] Found parallel - /usr/local/bin/parallel [01:17:55] Found freebayes - /usr/local/bin/freebayes [01:17:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:17:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:17:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:17:55] Found vcfuniq - /usr/local/bin/vcfuniq [01:17:55] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:17:55] Found gzip - /bin/gzip [01:17:55] Found vt - /usr/local/bin/vt [01:17:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:17:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:17:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:17:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:17:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:17:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:17:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:17:56] Please supply a reference FASTA/GBK/EMBL file with --reference
1[23:18:36] This is snippy 4.6.0
Show full stderr[23:18:36] This is snippy 4.6.0 [23:18:36] Written by Torsten Seemann [23:18:36] Obtained from https://github.com/tseemann/snippy [23:18:36] Detected operating system: linux [23:18:36] Enabling bundled linux tools. [23:18:36] Found bwa - /usr/local/bin/bwa [23:18:36] Found bcftools - /usr/local/bin/bcftools [23:18:36] Found samtools - /usr/local/bin/samtools [23:18:36] Found java - /usr/local/bin/java [23:18:36] Found snpEff - /usr/local/bin/snpEff [23:18:36] Found samclip - /usr/local/bin/samclip [23:18:36] Found seqtk - /usr/local/bin/seqtk [23:18:36] Found parallel - /usr/local/bin/parallel [23:18:36] Found freebayes - /usr/local/bin/freebayes [23:18:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [23:18:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [23:18:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [23:18:36] Found vcfuniq - /usr/local/bin/vcfuniq [23:18:36] Found vcffirstheader - /usr/local/bin/vcffirstheader [23:18:36] Found gzip - /bin/gzip [23:18:36] Found vt - /usr/local/bin/vt [23:18:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [23:18:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [23:18:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [23:18:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [23:18:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [23:18:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [23:18:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [23:18:39] Please supply a reference FASTA/GBK/EMBL file with --reference
1[23:35:06] This is snippy 4.6.0
Show full stderr[23:35:06] This is snippy 4.6.0 [23:35:06] Written by Torsten Seemann [23:35:06] Obtained from https://github.com/tseemann/snippy [23:35:06] Detected operating system: linux [23:35:06] Enabling bundled linux tools. [23:35:06] Found bwa - /usr/local/bin/bwa [23:35:06] Found bcftools - /usr/local/bin/bcftools [23:35:06] Found samtools - /usr/local/bin/samtools [23:35:06] Found java - /usr/local/bin/java [23:35:06] Found snpEff - /usr/local/bin/snpEff [23:35:06] Found samclip - /usr/local/bin/samclip [23:35:06] Found seqtk - /usr/local/bin/seqtk [23:35:06] Found parallel - /usr/local/bin/parallel [23:35:06] Found freebayes - /usr/local/bin/freebayes [23:35:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [23:35:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [23:35:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [23:35:06] Found vcfuniq - /usr/local/bin/vcfuniq [23:35:06] Found vcffirstheader - /usr/local/bin/vcffirstheader [23:35:06] Found gzip - /bin/gzip [23:35:06] Found vt - /usr/local/bin/vt [23:35:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [23:35:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [23:35:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [23:35:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [23:35:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [23:35:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [23:35:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [23:35:07] Please supply a reference FASTA/GBK/EMBL file with --reference
1[23:58:42] This is snippy 4.6.0
Show full stderr[23:58:42] This is snippy 4.6.0 [23:58:42] Written by Torsten Seemann [23:58:42] Obtained from https://github.com/tseemann/snippy [23:58:42] Detected operating system: linux [23:58:42] Enabling bundled linux tools. [23:58:42] Found bwa - /usr/local/bin/bwa [23:58:42] Found bcftools - /usr/local/bin/bcftools [23:58:42] Found samtools - /usr/local/bin/samtools [23:58:42] Found java - /usr/local/bin/java [23:58:42] Found snpEff - /usr/local/bin/snpEff [23:58:42] Found samclip - /usr/local/bin/samclip [23:58:42] Found seqtk - /usr/local/bin/seqtk [23:58:42] Found parallel - /usr/local/bin/parallel [23:58:42] Found freebayes - /usr/local/bin/freebayes [23:58:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [23:58:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [23:58:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [23:58:42] Found vcfuniq - /usr/local/bin/vcfuniq [23:58:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [23:58:42] Found gzip - /bin/gzip [23:58:42] Found vt - /usr/local/bin/vt [23:58:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [23:58:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [23:58:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [23:58:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [23:58:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [23:58:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [23:58:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [23:58:43] Please supply a reference FASTA/GBK/EMBL file with --reference
1[20:30:48] This is snippy 4.6.0
Show full stderr[20:30:48] This is snippy 4.6.0 [20:30:48] Written by Torsten Seemann [20:30:48] Obtained from https://github.com/tseemann/snippy [20:30:48] Detected operating system: linux [20:30:48] Enabling bundled linux tools. [20:30:48] Found bwa - /usr/local/bin/bwa [20:30:48] Found bcftools - /usr/local/bin/bcftools [20:30:48] Found samtools - /usr/local/bin/samtools [20:30:48] Found java - /usr/local/bin/java [20:30:48] Found snpEff - /usr/local/bin/snpEff [20:30:48] Found samclip - /usr/local/bin/samclip [20:30:48] Found seqtk - /usr/local/bin/seqtk [20:30:48] Found parallel - /usr/local/bin/parallel [20:30:48] Found freebayes - /usr/local/bin/freebayes [20:30:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [20:30:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [20:30:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [20:30:48] Found vcfuniq - /usr/local/bin/vcfuniq [20:30:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [20:30:48] Found gzip - /bin/gzip [20:30:48] Found vt - /usr/local/bin/vt [20:30:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [20:30:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [20:30:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [20:30:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [20:30:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [20:30:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [20:30:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [20:30:49] Please supply a reference FASTA/GBK/EMBL file with --reference
1[23:59:36] This is snippy 4.6.0
Show full stderr[23:59:36] This is snippy 4.6.0 [23:59:36] Written by Torsten Seemann [23:59:36] Obtained from https://github.com/tseemann/snippy [23:59:36] Detected operating system: linux [23:59:36] Enabling bundled linux tools. [23:59:36] Found bwa - /usr/local/bin/bwa [23:59:36] Found bcftools - /usr/local/bin/bcftools [23:59:36] Found samtools - /usr/local/bin/samtools [23:59:36] Found java - /usr/local/bin/java [23:59:36] Found snpEff - /usr/local/bin/snpEff [23:59:36] Found samclip - /usr/local/bin/samclip [23:59:36] Found seqtk - /usr/local/bin/seqtk [23:59:36] Found parallel - /usr/local/bin/parallel [23:59:36] Found freebayes - /usr/local/bin/freebayes [23:59:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [23:59:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [23:59:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [23:59:36] Found vcfuniq - /usr/local/bin/vcfuniq [23:59:36] Found vcffirstheader - /usr/local/bin/vcffirstheader [23:59:36] Found gzip - /bin/gzip [23:59:36] Found vt - /usr/local/bin/vt [23:59:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [23:59:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [23:59:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [23:59:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [23:59:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [23:59:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [23:59:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [23:59:37] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:43:25] This is snippy 4.6.0
Show full stderr[00:43:25] This is snippy 4.6.0 [00:43:25] Written by Torsten Seemann [00:43:25] Obtained from https://github.com/tseemann/snippy [00:43:25] Detected operating system: linux [00:43:25] Enabling bundled linux tools. [00:43:25] Found bwa - /usr/local/bin/bwa [00:43:25] Found bcftools - /usr/local/bin/bcftools [00:43:25] Found samtools - /usr/local/bin/samtools [00:43:25] Found java - /usr/local/bin/java [00:43:25] Found snpEff - /usr/local/bin/snpEff [00:43:25] Found samclip - /usr/local/bin/samclip [00:43:25] Found seqtk - /usr/local/bin/seqtk [00:43:25] Found parallel - /usr/local/bin/parallel [00:43:25] Found freebayes - /usr/local/bin/freebayes [00:43:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:43:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:43:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:43:25] Found vcfuniq - /usr/local/bin/vcfuniq [00:43:25] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:43:25] Found gzip - /bin/gzip [00:43:25] Found vt - /usr/local/bin/vt [00:43:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:43:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:43:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:43:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:43:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:43:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:43:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:43:26] Please supply a reference FASTA/GBK/EMBL file with --reference
1[09:47:01] This is snippy 4.6.0
Show full stderr[09:47:01] This is snippy 4.6.0 [09:47:01] Written by Torsten Seemann [09:47:01] Obtained from https://github.com/tseemann/snippy [09:47:01] Detected operating system: linux [09:47:01] Enabling bundled linux tools. [09:47:01] Found bwa - /usr/local/bin/bwa [09:47:01] Found bcftools - /usr/local/bin/bcftools [09:47:01] Found samtools - /usr/local/bin/samtools [09:47:01] Found java - /usr/local/bin/java [09:47:01] Found snpEff - /usr/local/bin/snpEff [09:47:01] Found samclip - /usr/local/bin/samclip [09:47:01] Found seqtk - /usr/local/bin/seqtk [09:47:01] Found parallel - /usr/local/bin/parallel [09:47:01] Found freebayes - /usr/local/bin/freebayes [09:47:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [09:47:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [09:47:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [09:47:01] Found vcfuniq - /usr/local/bin/vcfuniq [09:47:01] Found vcffirstheader - /usr/local/bin/vcffirstheader [09:47:01] Found gzip - /bin/gzip [09:47:01] Found vt - /usr/local/bin/vt [09:47:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [09:47:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [09:47:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [09:47:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [09:47:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [09:47:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [09:47:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [09:47:02] Using reference: /jetstream2/scratch/main/jobs/72478623/inputs/dataset_d3c82029-edc2-407d-bfbf-3c19136e7bbb.dat [09:47:02] Treating reference as 'fasta' format. [09:47:02] Will use 1 CPU cores. [09:47:02] Using read file: /jetstream2/scratch/main/jobs/72478623/inputs/dataset_63e50c05-a152-4847-9df5-b0c6a4cb45df.dat [09:47:02] Using read file: /jetstream2/scratch/main/jobs/72478623/inputs/dataset_63e50c05-a152-4847-9df5-b0c6a4cb45df.dat [09:47:02] Creating folder: HUAS_MG91 [09:47:02] Changing working directory: HUAS_MG91 [09:47:02] Creating reference folder: reference [09:47:02] Extracting FASTA and GFF from reference. [09:47:03] Wrote 3 sequences to ref.fa [09:47:03] Wrote 0 features to ref.gff [09:47:03] Freebayes will process 1 chunks of 9205924 bp, 1 chunks at a time. [09:47:03] Using BAM RG (Read Group) ID: HUAS_MG91 [09:47:03] Running: samtools faidx reference/ref.fa 2>> snps.log [09:47:03] Running: bwa index reference/ref.fa 2>> snps.log [09:47:05] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [09:47:05] Running: ln -sf reference/ref.fa . 2>> snps.log [09:47:05] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [09:47:05] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [09:47:05] Running: bwa mem -Y -M -R '@RG\tID:HUAS_MG91\tSM:HUAS_MG91' -t 1 reference/ref.fa /jetstream2/scratch/main/jobs/72478623/inputs/dataset_63e50c05-a152-4847-9df5-b0c6a4cb45df.dat /jetstream2/scratch/main/jobs/72478623/inputs/dataset_63e50c05-a152-4847-9df5-b0c6a4cb45df.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/72478623/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/72478623/tmp --threads 0 -m 12000M | samtools markdup -T /jetstream2/scratch/main/jobs/72478623/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loadin
1[09:48:40] This is snippy 4.6.0
Show full stderr[09:48:40] This is snippy 4.6.0 [09:48:40] Written by Torsten Seemann [09:48:40] Obtained from https://github.com/tseemann/snippy [09:48:40] Detected operating system: linux [09:48:40] Enabling bundled linux tools. [09:48:40] Found bwa - /usr/local/bin/bwa [09:48:40] Found bcftools - /usr/local/bin/bcftools [09:48:40] Found samtools - /usr/local/bin/samtools [09:48:40] Found java - /usr/local/bin/java [09:48:40] Found snpEff - /usr/local/bin/snpEff [09:48:40] Found samclip - /usr/local/bin/samclip [09:48:40] Found seqtk - /usr/local/bin/seqtk [09:48:40] Found parallel - /usr/local/bin/parallel [09:48:40] Found freebayes - /usr/local/bin/freebayes [09:48:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [09:48:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [09:48:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [09:48:40] Found vcfuniq - /usr/local/bin/vcfuniq [09:48:40] Found vcffirstheader - /usr/local/bin/vcffirstheader [09:48:40] Found gzip - /bin/gzip [09:48:40] Found vt - /usr/local/bin/vt [09:48:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [09:48:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [09:48:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [09:48:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [09:48:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [09:48:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [09:48:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [09:48:41] Using reference: /jetstream2/scratch/main/jobs/72478624/inputs/dataset_d3c82029-edc2-407d-bfbf-3c19136e7bbb.dat [09:48:41] Treating reference as 'fasta' format. [09:48:41] Will use 1 CPU cores. [09:48:41] Using read file: /jetstream2/scratch/main/jobs/72478624/inputs/dataset_89739e6d-721b-419b-ae5c-67c39031ebc2.dat [09:48:41] Using read file: /jetstream2/scratch/main/jobs/72478624/inputs/dataset_89739e6d-721b-419b-ae5c-67c39031ebc2.dat [09:48:41] Creating folder: GIMV4_001 [09:48:41] Changing working directory: GIMV4_001 [09:48:41] Creating reference folder: reference [09:48:41] Extracting FASTA and GFF from reference. [09:48:42] Wrote 3 sequences to ref.fa [09:48:42] Wrote 0 features to ref.gff [09:48:42] Freebayes will process 1 chunks of 9205924 bp, 1 chunks at a time. [09:48:42] Using BAM RG (Read Group) ID: GIMV4_001 [09:48:42] Running: samtools faidx reference/ref.fa 2>> snps.log [09:48:42] Running: bwa index reference/ref.fa 2>> snps.log [09:48:44] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [09:48:44] Running: ln -sf reference/ref.fa . 2>> snps.log [09:48:44] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [09:48:44] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [09:48:44] Running: bwa mem -Y -M -R '@RG\tID:GIMV4_001\tSM:GIMV4_001' -t 1 reference/ref.fa /jetstream2/scratch/main/jobs/72478624/inputs/dataset_89739e6d-721b-419b-ae5c-67c39031ebc2.dat /jetstream2/scratch/main/jobs/72478624/inputs/dataset_89739e6d-721b-419b-ae5c-67c39031ebc2.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/72478624/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/72478624/tmp --threads 0 -m 12000M | samtools markdup -T /jetstream2/scratch/main/jobs/72478624/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loadin
1[09:55:29] This is snippy 4.6.0
Show full stderr[09:55:29] This is snippy 4.6.0 [09:55:29] Written by Torsten Seemann [09:55:29] Obtained from https://github.com/tseemann/snippy [09:55:29] Detected operating system: linux [09:55:29] Enabling bundled linux tools. [09:55:29] Found bwa - /usr/local/bin/bwa [09:55:29] Found bcftools - /usr/local/bin/bcftools [09:55:29] Found samtools - /usr/local/bin/samtools [09:55:29] Found java - /usr/local/bin/java [09:55:29] Found snpEff - /usr/local/bin/snpEff [09:55:29] Found samclip - /usr/local/bin/samclip [09:55:29] Found seqtk - /usr/local/bin/seqtk [09:55:29] Found parallel - /usr/local/bin/parallel [09:55:29] Found freebayes - /usr/local/bin/freebayes [09:55:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [09:55:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [09:55:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [09:55:29] Found vcfuniq - /usr/local/bin/vcfuniq [09:55:29] Found vcffirstheader - /usr/local/bin/vcffirstheader [09:55:29] Found gzip - /bin/gzip [09:55:29] Found vt - /usr/local/bin/vt [09:55:29] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [09:55:29] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [09:55:29] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [09:55:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [09:55:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [09:55:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [09:55:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [09:55:31] Using reference: /jetstream2/scratch/main/jobs/72478625/inputs/dataset_d3c82029-edc2-407d-bfbf-3c19136e7bbb.dat [09:55:31] Treating reference as 'fasta' format. [09:55:31] Will use 1 CPU cores. [09:55:31] Using read file: /jetstream2/scratch/main/jobs/72478625/inputs/dataset_fcfb932c-4228-476f-9c0a-d2c9c2616e55.dat [09:55:31] Using read file: /jetstream2/scratch/main/jobs/72478625/inputs/dataset_fcfb932c-4228-476f-9c0a-d2c9c2616e55.dat [09:55:31] Creating folder: DSM_41954 [09:55:31] Changing working directory: DSM_41954 [09:55:31] Creating reference folder: reference [09:55:31] Extracting FASTA and GFF from reference. [09:55:31] Wrote 3 sequences to ref.fa [09:55:31] Wrote 0 features to ref.gff [09:55:31] Freebayes will process 1 chunks of 9205924 bp, 1 chunks at a time. [09:55:31] Using BAM RG (Read Group) ID: DSM_41954 [09:55:31] Running: samtools faidx reference/ref.fa 2>> snps.log [09:55:32] Running: bwa index reference/ref.fa 2>> snps.log [09:55:34] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [09:55:34] Running: ln -sf reference/ref.fa . 2>> snps.log [09:55:34] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [09:55:34] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [09:55:34] Running: bwa mem -Y -M -R '@RG\tID:DSM_41954\tSM:DSM_41954' -t 1 reference/ref.fa /jetstream2/scratch/main/jobs/72478625/inputs/dataset_fcfb932c-4228-476f-9c0a-d2c9c2616e55.dat /jetstream2/scratch/main/jobs/72478625/inputs/dataset_fcfb932c-4228-476f-9c0a-d2c9c2616e55.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/72478625/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/72478625/tmp --threads 0 -m 12000M | samtools markdup -T /jetstream2/scratch/main/jobs/72478625/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loadin
1[10:06:21] This is snippy 4.6.0
Show full stderr[10:06:21] This is snippy 4.6.0 [10:06:21] Written by Torsten Seemann [10:06:21] Obtained from https://github.com/tseemann/snippy [10:06:21] Detected operating system: linux [10:06:21] Enabling bundled linux tools. [10:06:21] Found bwa - /usr/local/bin/bwa [10:06:21] Found bcftools - /usr/local/bin/bcftools [10:06:21] Found samtools - /usr/local/bin/samtools [10:06:21] Found java - /usr/local/bin/java [10:06:21] Found snpEff - /usr/local/bin/snpEff [10:06:21] Found samclip - /usr/local/bin/samclip [10:06:21] Found seqtk - /usr/local/bin/seqtk [10:06:21] Found parallel - /usr/local/bin/parallel [10:06:21] Found freebayes - /usr/local/bin/freebayes [10:06:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [10:06:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [10:06:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [10:06:21] Found vcfuniq - /usr/local/bin/vcfuniq [10:06:21] Found vcffirstheader - /usr/local/bin/vcffirstheader [10:06:21] Found gzip - /bin/gzip [10:06:21] Found vt - /usr/local/bin/vt [10:06:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [10:06:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [10:06:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [10:06:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [10:06:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [10:06:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [10:06:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [10:06:22] Using reference: /jetstream2/scratch/main/jobs/72478626/inputs/dataset_d3c82029-edc2-407d-bfbf-3c19136e7bbb.dat [10:06:22] Treating reference as 'fasta' format. [10:06:22] Will use 1 CPU cores. [10:06:22] Using read file: /jetstream2/scratch/main/jobs/72478626/inputs/dataset_ffcdec99-376b-4a14-addb-2ad3776ef7ec.dat [10:06:22] Using read file: /jetstream2/scratch/main/jobs/72478626/inputs/dataset_ffcdec99-376b-4a14-addb-2ad3776ef7ec.dat [10:06:22] Creating folder: DSM_41771 [10:06:22] Changing working directory: DSM_41771 [10:06:22] Creating reference folder: reference [10:06:22] Extracting FASTA and GFF from reference. [10:06:23] Wrote 3 sequences to ref.fa [10:06:23] Wrote 0 features to ref.gff [10:06:23] Freebayes will process 1 chunks of 9205924 bp, 1 chunks at a time. [10:06:23] Using BAM RG (Read Group) ID: DSM_41771 [10:06:23] Running: samtools faidx reference/ref.fa 2>> snps.log [10:06:23] Running: bwa index reference/ref.fa 2>> snps.log [10:06:26] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [10:06:26] Running: ln -sf reference/ref.fa . 2>> snps.log [10:06:26] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [10:06:26] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [10:06:26] Running: bwa mem -Y -M -R '@RG\tID:DSM_41771\tSM:DSM_41771' -t 1 reference/ref.fa /jetstream2/scratch/main/jobs/72478626/inputs/dataset_ffcdec99-376b-4a14-addb-2ad3776ef7ec.dat /jetstream2/scratch/main/jobs/72478626/inputs/dataset_ffcdec99-376b-4a14-addb-2ad3776ef7ec.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/72478626/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/72478626/tmp --threads 0 -m 12000M | samtools markdup -T /jetstream2/scratch/main/jobs/72478626/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loadin
1[09:38:17] This is snippy 4.6.0
Show full stderr[09:38:17] This is snippy 4.6.0 [09:38:17] Written by Torsten Seemann [09:38:17] Obtained from https://github.com/tseemann/snippy [09:38:17] Detected operating system: linux [09:38:17] Enabling bundled linux tools. [09:38:17] Found bwa - /usr/local/bin/bwa [09:38:17] Found bcftools - /usr/local/bin/bcftools [09:38:17] Found samtools - /usr/local/bin/samtools [09:38:17] Found java - /usr/local/bin/java [09:38:17] Found snpEff - /usr/local/bin/snpEff [09:38:17] Found samclip - /usr/local/bin/samclip [09:38:17] Found seqtk - /usr/local/bin/seqtk [09:38:17] Found parallel - /usr/local/bin/parallel [09:38:17] Found freebayes - /usr/local/bin/freebayes [09:38:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [09:38:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [09:38:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [09:38:18] Found vcfuniq - /usr/local/bin/vcfuniq [09:38:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [09:38:18] Found gzip - /bin/gzip [09:38:18] Found vt - /usr/local/bin/vt [09:38:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [09:38:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [09:38:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [09:38:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [09:38:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [09:38:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [09:38:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [09:38:20] Using reference: /jetstream2/scratch/main/jobs/72478632/inputs/dataset_d3c82029-edc2-407d-bfbf-3c19136e7bbb.dat [09:38:20] Treating reference as 'fasta' format. [09:38:20] Will use 1 CPU cores. [09:38:20] Using read file: /jetstream2/scratch/main/jobs/72478632/inputs/dataset_5b72747f-cdbd-401a-9457-c521691ae78d.dat [09:38:20] Using read file: /jetstream2/scratch/main/jobs/72478632/inputs/dataset_5b72747f-cdbd-401a-9457-c521691ae78d.dat [09:38:20] Creating folder: BH_MK_02 [09:38:20] Changing working directory: BH_MK_02 [09:38:20] Creating reference folder: reference [09:38:20] Extracting FASTA and GFF from reference. [09:38:21] Wrote 3 sequences to ref.fa [09:38:21] Wrote 0 features to ref.gff [09:38:21] Freebayes will process 1 chunks of 9205924 bp, 1 chunks at a time. [09:38:21] Using BAM RG (Read Group) ID: BH_MK_02 [09:38:21] Running: samtools faidx reference/ref.fa 2>> snps.log [09:38:21] Running: bwa index reference/ref.fa 2>> snps.log [09:38:24] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [09:38:24] Running: ln -sf reference/ref.fa . 2>> snps.log [09:38:24] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [09:38:24] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [09:38:24] Running: bwa mem -Y -M -R '@RG\tID:BH_MK_02\tSM:BH_MK_02' -t 1 reference/ref.fa /jetstream2/scratch/main/jobs/72478632/inputs/dataset_5b72747f-cdbd-401a-9457-c521691ae78d.dat /jetstream2/scratch/main/jobs/72478632/inputs/dataset_5b72747f-cdbd-401a-9457-c521691ae78d.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/72478632/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/72478632/tmp --threads 0 -m 12000M | samtools markdup -T /jetstream2/scratch/main/jobs/72478632/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: r
1[09:46:02] This is snippy 4.6.0
Show full stderr[09:46:02] This is snippy 4.6.0 [09:46:02] Written by Torsten Seemann [09:46:02] Obtained from https://github.com/tseemann/snippy [09:46:02] Detected operating system: linux [09:46:02] Enabling bundled linux tools. [09:46:02] Found bwa - /usr/local/bin/bwa [09:46:02] Found bcftools - /usr/local/bin/bcftools [09:46:02] Found samtools - /usr/local/bin/samtools [09:46:02] Found java - /usr/local/bin/java [09:46:02] Found snpEff - /usr/local/bin/snpEff [09:46:02] Found samclip - /usr/local/bin/samclip [09:46:02] Found seqtk - /usr/local/bin/seqtk [09:46:02] Found parallel - /usr/local/bin/parallel [09:46:02] Found freebayes - /usr/local/bin/freebayes [09:46:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [09:46:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [09:46:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [09:46:02] Found vcfuniq - /usr/local/bin/vcfuniq [09:46:02] Found vcffirstheader - /usr/local/bin/vcffirstheader [09:46:02] Found gzip - /bin/gzip [09:46:02] Found vt - /usr/local/bin/vt [09:46:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [09:46:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [09:46:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [09:46:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [09:46:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [09:46:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [09:46:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [09:46:06] Using reference: /jetstream2/scratch/main/jobs/72478636/inputs/dataset_d3c82029-edc2-407d-bfbf-3c19136e7bbb.dat [09:46:06] Treating reference as 'fasta' format. [09:46:06] Will use 1 CPU cores. [09:46:06] Using read file: /jetstream2/scratch/main/jobs/72478636/inputs/dataset_fa7f794c-ea76-43bb-8571-98ff1b98be6f.dat [09:46:06] Using read file: /jetstream2/scratch/main/jobs/72478636/inputs/dataset_fa7f794c-ea76-43bb-8571-98ff1b98be6f.dat [09:46:06] Creating folder: ATCC_14922 [09:46:06] Changing working directory: ATCC_14922 [09:46:06] Creating reference folder: reference [09:46:06] Extracting FASTA and GFF from reference. [09:46:07] Wrote 3 sequences to ref.fa [09:46:07] Wrote 0 features to ref.gff [09:46:07] Freebayes will process 1 chunks of 9205924 bp, 1 chunks at a time. [09:46:07] Using BAM RG (Read Group) ID: ATCC_14922 [09:46:07] Running: samtools faidx reference/ref.fa 2>> snps.log [09:46:07] Running: bwa index reference/ref.fa 2>> snps.log [09:46:10] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [09:46:10] Running: ln -sf reference/ref.fa . 2>> snps.log [09:46:10] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [09:46:10] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [09:46:10] Running: bwa mem -Y -M -R '@RG\tID:ATCC_14922\tSM:ATCC_14922' -t 1 reference/ref.fa /jetstream2/scratch/main/jobs/72478636/inputs/dataset_fa7f794c-ea76-43bb-8571-98ff1b98be6f.dat /jetstream2/scratch/main/jobs/72478636/inputs/dataset_fa7f794c-ea76-43bb-8571-98ff1b98be6f.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/72478636/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/72478636/tmp --threads 0 -m 12000M | samtools markdup -T /jetstream2/scratch/main/jobs/72478636/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] L
1[10:00:06] This is snippy 4.6.0
Show full stderr[10:00:06] This is snippy 4.6.0 [10:00:06] Written by Torsten Seemann [10:00:06] Obtained from https://github.com/tseemann/snippy [10:00:06] Detected operating system: linux [10:00:06] Enabling bundled linux tools. [10:00:06] Found bwa - /usr/local/bin/bwa [10:00:06] Found bcftools - /usr/local/bin/bcftools [10:00:06] Found samtools - /usr/local/bin/samtools [10:00:06] Found java - /usr/local/bin/java [10:00:06] Found snpEff - /usr/local/bin/snpEff [10:00:06] Found samclip - /usr/local/bin/samclip [10:00:06] Found seqtk - /usr/local/bin/seqtk [10:00:06] Found parallel - /usr/local/bin/parallel [10:00:06] Found freebayes - /usr/local/bin/freebayes [10:00:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [10:00:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [10:00:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [10:00:06] Found vcfuniq - /usr/local/bin/vcfuniq [10:00:06] Found vcffirstheader - /usr/local/bin/vcffirstheader [10:00:06] Found gzip - /bin/gzip [10:00:06] Found vt - /usr/local/bin/vt [10:00:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [10:00:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [10:00:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [10:00:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [10:00:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [10:00:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [10:00:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [10:00:07] Using reference: /jetstream2/scratch/main/jobs/72478640/inputs/dataset_d3c82029-edc2-407d-bfbf-3c19136e7bbb.dat [10:00:07] Treating reference as 'fasta' format. [10:00:07] Will use 1 CPU cores. [10:00:07] Using read file: /jetstream2/scratch/main/jobs/72478640/inputs/dataset_bd15df9e-663f-4f70-bb5f-fef1ca7d60f1.dat [10:00:07] Using read file: /jetstream2/scratch/main/jobs/72478640/inputs/dataset_bd15df9e-663f-4f70-bb5f-fef1ca7d60f1.dat [10:00:07] Creating folder: 452 [10:00:07] Changing working directory: 452 [10:00:07] Creating reference folder: reference [10:00:07] Extracting FASTA and GFF from reference. [10:00:08] Wrote 3 sequences to ref.fa [10:00:08] Wrote 0 features to ref.gff [10:00:08] Freebayes will process 1 chunks of 9205924 bp, 1 chunks at a time. [10:00:08] Using BAM RG (Read Group) ID: 452 [10:00:08] Running: samtools faidx reference/ref.fa 2>> snps.log [10:00:08] Running: bwa index reference/ref.fa 2>> snps.log [10:00:11] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [10:00:11] Running: ln -sf reference/ref.fa . 2>> snps.log [10:00:11] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [10:00:11] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [10:00:11] Running: bwa mem -Y -M -R '@RG\tID:452\tSM:452' -t 1 reference/ref.fa /jetstream2/scratch/main/jobs/72478640/inputs/dataset_bd15df9e-663f-4f70-bb5f-fef1ca7d60f1.dat /jetstream2/scratch/main/jobs/72478640/inputs/dataset_bd15df9e-663f-4f70-bb5f-fef1ca7d60f1.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/72478640/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/72478640/tmp --threads 0 -m 12000M | samtools markdup -T /jetstream2/scratch/main/jobs/72478640/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [M::bwa_idx_load_from_disk] read 0 ALT contigs [samc
1[10:00:17] This is snippy 4.6.0
Show full stderr[10:00:17] This is snippy 4.6.0 [10:00:17] Written by Torsten Seemann [10:00:17] Obtained from https://github.com/tseemann/snippy [10:00:17] Detected operating system: linux [10:00:17] Enabling bundled linux tools. [10:00:17] Found bwa - /usr/local/bin/bwa [10:00:17] Found bcftools - /usr/local/bin/bcftools [10:00:17] Found samtools - /usr/local/bin/samtools [10:00:17] Found java - /usr/local/bin/java [10:00:17] Found snpEff - /usr/local/bin/snpEff [10:00:17] Found samclip - /usr/local/bin/samclip [10:00:17] Found seqtk - /usr/local/bin/seqtk [10:00:17] Found parallel - /usr/local/bin/parallel [10:00:17] Found freebayes - /usr/local/bin/freebayes [10:00:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [10:00:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [10:00:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [10:00:17] Found vcfuniq - /usr/local/bin/vcfuniq [10:00:17] Found vcffirstheader - /usr/local/bin/vcffirstheader [10:00:17] Found gzip - /bin/gzip [10:00:18] Found vt - /usr/local/bin/vt [10:00:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [10:00:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [10:00:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [10:00:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [10:00:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [10:00:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [10:00:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [10:00:18] Using reference: /jetstream2/scratch/main/jobs/72479039/inputs/dataset_d3c82029-edc2-407d-bfbf-3c19136e7bbb.dat [10:00:18] Treating reference as 'fasta' format. [10:00:18] Will use 1 CPU cores. [10:00:18] Using read file: /jetstream2/scratch/main/jobs/72479039/inputs/dataset_918fb325-2c7e-4099-8f14-75c5948d1f0c.dat [10:00:18] Using read file: /jetstream2/scratch/main/jobs/72479039/inputs/dataset_918fb325-2c7e-4099-8f14-75c5948d1f0c.dat [10:00:18] Creating folder: Kala_fna [10:00:18] Changing working directory: Kala_fna [10:00:18] Creating reference folder: reference [10:00:18] Extracting FASTA and GFF from reference. [10:00:19] Wrote 3 sequences to ref.fa [10:00:19] Wrote 0 features to ref.gff [10:00:19] Freebayes will process 1 chunks of 9205924 bp, 1 chunks at a time. [10:00:19] Using BAM RG (Read Group) ID: Kala_fna [10:00:19] Running: samtools faidx reference/ref.fa 2>> snps.log [10:00:19] Running: bwa index reference/ref.fa 2>> snps.log [10:00:22] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [10:00:22] Running: ln -sf reference/ref.fa . 2>> snps.log [10:00:22] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [10:00:22] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [10:00:22] Running: bwa mem -Y -M -R '@RG\tID:Kala_fna\tSM:Kala_fna' -t 1 reference/ref.fa /jetstream2/scratch/main/jobs/72479039/inputs/dataset_918fb325-2c7e-4099-8f14-75c5948d1f0c.dat /jetstream2/scratch/main/jobs/72479039/inputs/dataset_918fb325-2c7e-4099-8f14-75c5948d1f0c.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/72479039/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/72479039/tmp --threads 0 -m 12000M | samtools markdup -T /jetstream2/scratch/main/jobs/72479039/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [M::bwa_idx_load_from_disk] re
1[10:03:31] This is snippy 4.6.0
Show full stderr[10:03:31] This is snippy 4.6.0 [10:03:31] Written by Torsten Seemann [10:03:31] Obtained from https://github.com/tseemann/snippy [10:03:31] Detected operating system: linux [10:03:31] Enabling bundled linux tools. [10:03:31] Found bwa - /usr/local/bin/bwa [10:03:31] Found bcftools - /usr/local/bin/bcftools [10:03:31] Found samtools - /usr/local/bin/samtools [10:03:31] Found java - /usr/local/bin/java [10:03:31] Found snpEff - /usr/local/bin/snpEff [10:03:31] Found samclip - /usr/local/bin/samclip [10:03:31] Found seqtk - /usr/local/bin/seqtk [10:03:31] Found parallel - /usr/local/bin/parallel [10:03:31] Found freebayes - /usr/local/bin/freebayes [10:03:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [10:03:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [10:03:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [10:03:31] Found vcfuniq - /usr/local/bin/vcfuniq [10:03:31] Found vcffirstheader - /usr/local/bin/vcffirstheader [10:03:31] Found gzip - /bin/gzip [10:03:31] Found vt - /usr/local/bin/vt [10:03:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [10:03:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [10:03:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [10:03:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [10:03:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [10:03:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [10:03:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [10:03:35] Using reference: /jetstream2/scratch/main/jobs/72479043/inputs/dataset_d3c82029-edc2-407d-bfbf-3c19136e7bbb.dat [10:03:35] Treating reference as 'fasta' format. [10:03:35] Will use 1 CPU cores. [10:03:35] Using read file: /jetstream2/scratch/main/jobs/72479043/inputs/dataset_fcfb932c-4228-476f-9c0a-d2c9c2616e55.dat [10:03:35] Using read file: /jetstream2/scratch/main/jobs/72479043/inputs/dataset_fcfb932c-4228-476f-9c0a-d2c9c2616e55.dat [10:03:35] Creating folder: DSM_41954_fna [10:03:35] Changing working directory: DSM_41954_fna [10:03:35] Creating reference folder: reference [10:03:35] Extracting FASTA and GFF from reference. [10:03:35] Wrote 3 sequences to ref.fa [10:03:35] Wrote 0 features to ref.gff [10:03:35] Freebayes will process 1 chunks of 9205924 bp, 1 chunks at a time. [10:03:35] Using BAM RG (Read Group) ID: DSM_41954_fna [10:03:35] Running: samtools faidx reference/ref.fa 2>> snps.log [10:03:35] Running: bwa index reference/ref.fa 2>> snps.log [10:03:38] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [10:03:38] Running: ln -sf reference/ref.fa . 2>> snps.log [10:03:38] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [10:03:38] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [10:03:38] Running: bwa mem -Y -M -R '@RG\tID:DSM_41954_fna\tSM:DSM_41954_fna' -t 1 reference/ref.fa /jetstream2/scratch/main/jobs/72479043/inputs/dataset_fcfb932c-4228-476f-9c0a-d2c9c2616e55.dat /jetstream2/scratch/main/jobs/72479043/inputs/dataset_fcfb932c-4228-476f-9c0a-d2c9c2616e55.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/72479043/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/72479043/tmp --threads 0 -m 12000M | samtools markdup -T /jetstream2/scratch/main/jobs/72479043/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseeman
1[13:13:52] This is snippy 4.6.0
Show full stderr[13:13:52] This is snippy 4.6.0 [13:13:52] Written by Torsten Seemann [13:13:52] Obtained from https://github.com/tseemann/snippy [13:13:52] Detected operating system: linux [13:13:52] Enabling bundled linux tools. [13:13:52] Found bwa - /usr/local/bin/bwa [13:13:52] Found bcftools - /usr/local/bin/bcftools [13:13:52] Found samtools - /usr/local/bin/samtools [13:13:52] Found java - /usr/local/bin/java [13:13:52] Found snpEff - /usr/local/bin/snpEff [13:13:52] Found samclip - /usr/local/bin/samclip [13:13:52] Found seqtk - /usr/local/bin/seqtk [13:13:52] Found parallel - /usr/local/bin/parallel [13:13:52] Found freebayes - /usr/local/bin/freebayes [13:13:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [13:13:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [13:13:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [13:13:52] Found vcfuniq - /usr/local/bin/vcfuniq [13:13:52] Found vcffirstheader - /usr/local/bin/vcffirstheader [13:13:52] Found gzip - /bin/gzip [13:13:52] Found vt - /usr/local/bin/vt [13:13:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [13:13:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [13:13:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [13:13:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [13:13:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [13:13:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [13:13:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [13:13:55] Using reference: /cvmfs/data.galaxyproject.org/byhand/hg38/seq/hg38full.fa [13:15:20] Treating reference as 'fasta' format. [13:15:20] Will use 1 CPU cores. [13:15:20] Using read file: /jetstream2/scratch/main/jobs/72614466/inputs/dataset_f965950b-ce9d-4e63-9a8c-09375be2a2a7.dat [13:15:20] Using read file: /jetstream2/scratch/main/jobs/72614466/inputs/dataset_f965950b-ce9d-4e63-9a8c-09375be2a2a7.dat [13:15:20] Creating folder: Y08757_1_fasta [13:15:20] Changing working directory: Y08757_1_fasta [13:15:20] Creating reference folder: reference [13:15:20] Extracting FASTA and GFF from reference. /jetstream2/scratch/main/jobs/72614466/tool_script.sh: line 23: 21 Killed snippy --outdir 'Y08757_1_fasta' --cpus ${GALAXY_SLOTS:-1} --ram $((${GALAXY_MEMORY_MB:-4096}/1024)) --ref 'ref.fna' --mapqual 60 --mincov 10 --minfrac 0.9 --minqual 100.0 --R1 '/jetstream2/scratch/main/jobs/72614466/inputs/dataset_f965950b-ce9d-4e63-9a8c-09375be2a2a7.dat' --R2 '/jetstream2/scratch/main/jobs/72614466/inputs/dataset_f965950b-ce9d-4e63-9a8c-09375be2a2a7.dat'
1[21:30:23] This is snippy 4.6.0
Show full stderr[21:30:23] This is snippy 4.6.0 [21:30:23] Written by Torsten Seemann [21:30:23] Obtained from https://github.com/tseemann/snippy [21:30:23] Detected operating system: linux [21:30:23] Enabling bundled linux tools. [21:30:23] Found bwa - /usr/local/bin/bwa [21:30:23] Found bcftools - /usr/local/bin/bcftools [21:30:23] Found samtools - /usr/local/bin/samtools [21:30:23] Found java - /usr/local/bin/java [21:30:23] Found snpEff - /usr/local/bin/snpEff [21:30:23] Found samclip - /usr/local/bin/samclip [21:30:23] Found seqtk - /usr/local/bin/seqtk [21:30:23] Found parallel - /usr/local/bin/parallel [21:30:23] Found freebayes - /usr/local/bin/freebayes [21:30:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:30:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:30:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:30:23] Found vcfuniq - /usr/local/bin/vcfuniq [21:30:23] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:30:23] Found gzip - /bin/gzip [21:30:23] Found vt - /usr/local/bin/vt [21:30:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:30:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:30:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:30:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:30:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:30:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:30:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:30:24] Using reference: /corral4/main/objects/5/f/4/dataset_5f437c74-8e7d-4bb3-aa2d-514661d00074.dat [21:30:24] Treating reference as 'fasta' format. [21:30:24] Will use 1 CPU cores. [21:30:24] Using read file: /corral4/main/objects/5/e/8/dataset_5e802efb-d0bd-4b12-98e8-61f6df0fa797.dat [21:30:24] Creating folder: rpsJ_protein_21_563_fasta [21:30:24] Changing working directory: rpsJ_protein_21_563_fasta [21:30:24] Creating reference folder: reference [21:30:24] Extracting FASTA and GFF from reference. [21:30:25] Wrote 1 sequences to ref.fa [21:30:25] Wrote 0 features to ref.gff [21:30:25] Shredding /corral4/main/objects/5/e/8/dataset_5e802efb-d0bd-4b12-98e8-61f6df0fa797.dat into pseudo-reads ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Sequence is a protein. Cannot revcom. STACK: Error::throw STACK: Bio::Root::Root::throw /usr/local/lib/site_perl/5.26.2/Bio/Root/Root.pm:447 STACK: Bio::PrimarySeqI::_revcom_from_string /usr/local/lib/site_perl/5.26.2/Bio/PrimarySeqI.pm:401 STACK: Bio::PrimarySeqI::revcom /usr/local/lib/site_perl/5.26.2/Bio/PrimarySeqI.pm:391 STACK: /usr/local/bin/snippy:256 -----------------------------------------------------------
1[21:31:33] This is snippy 4.6.0
Show full stderr[21:31:33] This is snippy 4.6.0 [21:31:33] Written by Torsten Seemann [21:31:33] Obtained from https://github.com/tseemann/snippy [21:31:33] Detected operating system: linux [21:31:33] Enabling bundled linux tools. [21:31:33] Found bwa - /usr/local/bin/bwa [21:31:33] Found bcftools - /usr/local/bin/bcftools [21:31:33] Found samtools - /usr/local/bin/samtools [21:31:33] Found java - /usr/local/bin/java [21:31:33] Found snpEff - /usr/local/bin/snpEff [21:31:33] Found samclip - /usr/local/bin/samclip [21:31:33] Found seqtk - /usr/local/bin/seqtk [21:31:33] Found parallel - /usr/local/bin/parallel [21:31:33] Found freebayes - /usr/local/bin/freebayes [21:31:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:31:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:31:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:31:33] Found vcfuniq - /usr/local/bin/vcfuniq [21:31:33] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:31:33] Found gzip - /bin/gzip [21:31:33] Found vt - /usr/local/bin/vt [21:31:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:31:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:31:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:31:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:31:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:31:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:31:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:31:34] Using reference: /corral4/main/objects/5/f/4/dataset_5f437c74-8e7d-4bb3-aa2d-514661d00074.dat [21:31:34] Treating reference as 'fasta' format. [21:31:34] Will use 1 CPU cores. [21:31:34] Using read file: /corral4/main/objects/5/f/4/dataset_5f437c74-8e7d-4bb3-aa2d-514661d00074.dat [21:31:34] Creating folder: rpsJ_wt_fasta [21:31:34] Changing working directory: rpsJ_wt_fasta [21:31:34] Creating reference folder: reference [21:31:34] Extracting FASTA and GFF from reference. [21:31:34] Wrote 1 sequences to ref.fa [21:31:34] Wrote 0 features to ref.gff [21:31:34] Shredding /corral4/main/objects/5/f/4/dataset_5f437c74-8e7d-4bb3-aa2d-514661d00074.dat into pseudo-reads ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Sequence is a protein. Cannot revcom. STACK: Error::throw STACK: Bio::Root::Root::throw /usr/local/lib/site_perl/5.26.2/Bio/Root/Root.pm:447 STACK: Bio::PrimarySeqI::_revcom_from_string /usr/local/lib/site_perl/5.26.2/Bio/PrimarySeqI.pm:401 STACK: Bio::PrimarySeqI::revcom /usr/local/lib/site_perl/5.26.2/Bio/PrimarySeqI.pm:391 STACK: /usr/local/bin/snippy:256 -----------------------------------------------------------
1[15:43:45] This is snippy 4.6.0
Show full stderr[15:43:45] This is snippy 4.6.0 [15:43:45] Written by Torsten Seemann [15:43:45] Obtained from https://github.com/tseemann/snippy [15:43:45] Detected operating system: linux [15:43:45] Enabling bundled linux tools. [15:43:45] Found bwa - /usr/local/bin/bwa [15:43:45] Found bcftools - /usr/local/bin/bcftools [15:43:45] Found samtools - /usr/local/bin/samtools [15:43:45] Found java - /usr/local/bin/java [15:43:45] Found snpEff - /usr/local/bin/snpEff [15:43:45] Found samclip - /usr/local/bin/samclip [15:43:45] Found seqtk - /usr/local/bin/seqtk [15:43:45] Found parallel - /usr/local/bin/parallel [15:43:45] Found freebayes - /usr/local/bin/freebayes [15:43:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [15:43:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [15:43:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [15:43:45] Found vcfuniq - /usr/local/bin/vcfuniq [15:43:45] Found vcffirstheader - /usr/local/bin/vcffirstheader [15:43:45] Found gzip - /bin/gzip [15:43:45] Found vt - /usr/local/bin/vt [15:43:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [15:43:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [15:43:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [15:43:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [15:43:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [15:43:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [15:43:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [15:43:49] Using reference: /jetstream2/scratch/main/jobs/72674863/inputs/dataset_ce41989f-7ee4-48c8-9529-f279bb8181e6.dat [15:43:49] Treating reference as 'fasta' format. [15:43:49] Will use 1 CPU cores. [15:43:49] Using read file: /jetstream2/scratch/main/jobs/72674863/inputs/dataset_e175473e-d18c-4c53-954e-2fbfddf8326f.dat [15:43:49] Using read file: /jetstream2/scratch/main/jobs/72674863/inputs/dataset_541c8783-b1da-4b37-b474-654565758f67.dat [15:43:49] Creating folder: X223RR_5_MIC_C_5_illumina_R1_fastq [15:43:49] Changing working directory: X223RR_5_MIC_C_5_illumina_R1_fastq [15:43:49] Creating reference folder: reference [15:43:49] Extracting FASTA and GFF from reference. [15:43:49] Wrote 1 sequences to ref.fa [15:43:49] Wrote 0 features to ref.gff [15:43:49] Freebayes will process 1 chunks of 5124326 bp, 1 chunks at a time. [15:43:49] Using BAM RG (Read Group) ID: X223RR_5_MIC_C_5_illumina_R1_fastq [15:43:49] Running: samtools faidx reference/ref.fa 2>> snps.log [15:43:49] Running: bwa index reference/ref.fa 2>> snps.log [15:43:51] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [15:43:51] Running: ln -sf reference/ref.fa . 2>> snps.log [15:43:51] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [15:43:51] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [15:43:51] Running: bwa mem -Y -M -R '@RG\tID:X223RR_5_MIC_C_5_illumina_R1_fastq\tSM:X223RR_5_MIC_C_5_illumina_R1_fastq' -t 1 reference/ref.fa /jetstream2/scratch/main/jobs/72674863/inputs/dataset_e175473e-d18c-4c53-954e-2fbfddf8326f.dat /jetstream2/scratch/main/jobs/72674863/inputs/dataset_541c8783-b1da-4b37-b474-654565758f67.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /jetstream2/scratch/main/jobs/72674863/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /jetstream2/scratch/main/jobs/72674863/tmp --threads 0 -m 12000M | samtools markdup -T /jetstream2/scratch/main/jobs/72674863/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_id
1[13:10:54] This is snippy 4.6.0
Show full stderr[13:10:54] This is snippy 4.6.0 [13:10:54] Written by Torsten Seemann [13:10:54] Obtained from https://github.com/tseemann/snippy [13:10:54] Detected operating system: linux [13:10:54] Enabling bundled linux tools. [13:10:54] Found bwa - /usr/local/bin/bwa [13:10:54] Found bcftools - /usr/local/bin/bcftools [13:10:54] Found samtools - /usr/local/bin/samtools [13:10:54] Found java - /usr/local/bin/java [13:10:54] Found snpEff - /usr/local/bin/snpEff [13:10:55] Found samclip - /usr/local/bin/samclip [13:10:55] Found seqtk - /usr/local/bin/seqtk [13:10:55] Found parallel - /usr/local/bin/parallel [13:10:55] Found freebayes - /usr/local/bin/freebayes [13:10:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [13:10:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [13:10:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [13:10:55] Found vcfuniq - /usr/local/bin/vcfuniq [13:10:55] Found vcffirstheader - /usr/local/bin/vcffirstheader [13:10:55] Found gzip - /bin/gzip [13:10:55] Found vt - /usr/local/bin/vt [13:10:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [13:10:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [13:10:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [13:10:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [13:10:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [13:10:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [13:10:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [13:10:55] Using reference: /corral4/main/objects/a/0/8/dataset_a08f00da-ba11-4ad8-99bd-2ff73d9144b8.dat [13:10:55] Treating reference as 'fasta' format. [13:10:55] Will use 1 CPU cores. [13:10:55] Using read file: /corral4/main/objects/3/f/c/dataset_3fc3c6fb-4b76-4b9f-9a2a-95a15be11d61.dat [13:10:55] Creating folder: Fa_summary_fasta [13:10:55] Changing working directory: Fa_summary_fasta [13:10:55] Creating reference folder: reference [13:10:55] Extracting FASTA and GFF from reference. [13:10:56] Duplicate sequence FJ445428|2007|SriLanka in /corral4/main/objects/a/0/8/dataset_a08f00da-ba11-4ad8-99bd-2ff73d9144b8.dat
1[14:16:52] This is snippy 4.6.0
Show full stderr[14:16:52] This is snippy 4.6.0 [14:16:52] Written by Torsten Seemann [14:16:52] Obtained from https://github.com/tseemann/snippy [14:16:52] Detected operating system: linux [14:16:52] Enabling bundled linux tools. [14:16:52] Found bwa - /usr/local/bin/bwa [14:16:52] Found bcftools - /usr/local/bin/bcftools [14:16:52] Found samtools - /usr/local/bin/samtools [14:16:52] Found java - /usr/local/bin/java [14:16:52] Found snpEff - /usr/local/bin/snpEff [14:16:52] Found samclip - /usr/local/bin/samclip [14:16:52] Found seqtk - /usr/local/bin/seqtk [14:16:52] Found parallel - /usr/local/bin/parallel [14:16:52] Found freebayes - /usr/local/bin/freebayes [14:16:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:16:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:16:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:16:52] Found vcfuniq - /usr/local/bin/vcfuniq [14:16:52] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:16:52] Found gzip - /bin/gzip [14:16:52] Found vt - /usr/local/bin/vt [14:16:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:16:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:16:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:16:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:16:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:16:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:16:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:16:53] Using reference: /corral4/main/objects/5/3/9/dataset_53992c10-f3f2-4370-8224-5403dd9cd3ea.dat [14:16:53] Treating reference as 'fasta' format. [14:16:53] Will use 1 CPU cores. [14:16:53] Using read file: /corral4/main/objects/1/7/c/dataset_17c5fbb2-e82f-4df4-805c-6028b009d325.dat [14:16:53] Creating folder: Fa_summary_fasta [14:16:53] Changing working directory: Fa_summary_fasta [14:16:53] Creating reference folder: reference [14:16:53] Extracting FASTA and GFF from reference. [14:16:54] Wrote 126 sequences to ref.fa [14:16:54] Wrote 0 features to ref.gff [14:16:54] Shredding /corral4/main/objects/1/7/c/dataset_17c5fbb2-e82f-4df4-805c-6028b009d325.dat into pseudo-reads [14:16:57] Wrote 268202 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [14:16:57] Freebayes will process 1 chunks of 1394678 bp, 1 chunks at a time. [14:16:57] Using BAM RG (Read Group) ID: Fa_summary_fasta [14:16:57] Running: samtools faidx reference/ref.fa 2>> snps.log [14:16:57] Running: bwa index reference/ref.fa 2>> snps.log [14:16:58] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [14:16:58] Running: ln -sf reference/ref.fa . 2>> snps.log [14:16:58] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [14:16:58] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [14:16:58] Running: bwa mem -Y -M -R '@RG\tID:Fa_summary_fasta\tSM:Fa_summary_fasta' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/752/72752915/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/752/72752915/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/752/72752915/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 126 sequences in reference/ref.fa.fai [M::process] read 4
1[18:43:45] This is snippy 4.6.0
Show full stderr[18:43:45] This is snippy 4.6.0 [18:43:45] Written by Torsten Seemann [18:43:45] Obtained from https://github.com/tseemann/snippy [18:43:45] Detected operating system: linux [18:43:45] Enabling bundled linux tools. [18:43:45] Found bwa - /usr/local/bin/bwa [18:43:45] Found bcftools - /usr/local/bin/bcftools [18:43:45] Found samtools - /usr/local/bin/samtools [18:43:45] Found java - /usr/local/bin/java [18:43:45] Found snpEff - /usr/local/bin/snpEff [18:43:45] Found samclip - /usr/local/bin/samclip [18:43:45] Found seqtk - /usr/local/bin/seqtk [18:43:45] Found parallel - /usr/local/bin/parallel [18:43:45] Found freebayes - /usr/local/bin/freebayes [18:43:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [18:43:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [18:43:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [18:43:45] Found vcfuniq - /usr/local/bin/vcfuniq [18:43:45] Found vcffirstheader - /usr/local/bin/vcffirstheader [18:43:45] Found gzip - /bin/gzip [18:43:45] Found vt - /usr/local/bin/vt [18:43:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [18:43:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [18:43:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [18:43:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [18:43:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [18:43:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [18:43:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [18:43:46] Using reference: /corral4/main/objects/d/7/6/dataset_d764c547-d517-4ce6-9e7c-25fb605e00f7.dat [18:43:46] Treating reference as 'genbank' format. [18:43:46] Will use 1 CPU cores. [18:43:46] Using read file: /corral4/main/objects/6/d/e/dataset_6de27930-ce42-4d00-bbc5-7c14263ab5b4.dat [18:43:46] Using read file: /corral4/main/objects/d/1/6/dataset_d16fac68-6b73-4781-86e3-48a6c0ad4fca.dat [18:43:46] Creating folder: 172_S96_L001_R1_001_fastq_gz [18:43:46] Changing working directory: 172_S96_L001_R1_001_fastq_gz [18:43:46] Creating reference folder: reference [18:43:46] Extracting FASTA and GFF from reference. Use of uninitialized value in uc at /usr/local/bin/snippy line 206, <GEN0> line 89. [18:43:46] Wrote 1 sequences to ref.fa [18:43:46] Wrote 0 features to ref.gff [18:43:46] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time. [18:43:46] Using BAM RG (Read Group) ID: 172_S96_L001_R1_001_fastq_gz [18:43:46] Running: samtools faidx reference/ref.fa 2>> snps.log [18:43:46] Error running command, check 172_S96_L001_R1_001_fastq_gz/snps.log
1[17:23:57] This is snippy 4.6.0
Show full stderr[17:23:57] This is snippy 4.6.0 [17:23:57] Written by Torsten Seemann [17:23:57] Obtained from https://github.com/tseemann/snippy [17:23:57] Detected operating system: linux [17:23:57] Enabling bundled linux tools. [17:23:57] Found bwa - /usr/local/bin/bwa [17:23:57] Found bcftools - /usr/local/bin/bcftools [17:23:57] Found samtools - /usr/local/bin/samtools [17:23:57] Found java - /usr/local/bin/java [17:23:57] Found snpEff - /usr/local/bin/snpEff [17:23:58] Found samclip - /usr/local/bin/samclip [17:23:58] Found seqtk - /usr/local/bin/seqtk [17:23:58] Found parallel - /usr/local/bin/parallel [17:23:58] Found freebayes - /usr/local/bin/freebayes [17:23:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:23:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:23:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:23:58] Found vcfuniq - /usr/local/bin/vcfuniq [17:23:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:23:58] Found gzip - /bin/gzip [17:23:58] Found vt - /usr/local/bin/vt [17:23:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:23:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:23:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:23:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:23:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:23:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:23:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:23:59] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:24:02] This is snippy 4.6.0
Show full stderr[17:24:02] This is snippy 4.6.0 [17:24:02] Written by Torsten Seemann [17:24:02] Obtained from https://github.com/tseemann/snippy [17:24:02] Detected operating system: linux [17:24:02] Enabling bundled linux tools. [17:24:02] Found bwa - /usr/local/bin/bwa [17:24:02] Found bcftools - /usr/local/bin/bcftools [17:24:02] Found samtools - /usr/local/bin/samtools [17:24:02] Found java - /usr/local/bin/java [17:24:02] Found snpEff - /usr/local/bin/snpEff [17:24:02] Found samclip - /usr/local/bin/samclip [17:24:02] Found seqtk - /usr/local/bin/seqtk [17:24:02] Found parallel - /usr/local/bin/parallel [17:24:02] Found freebayes - /usr/local/bin/freebayes [17:24:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:24:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:24:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:24:02] Found vcfuniq - /usr/local/bin/vcfuniq [17:24:02] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:24:02] Found gzip - /bin/gzip [17:24:02] Found vt - /usr/local/bin/vt [17:24:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:24:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:24:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:24:05] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:24:05] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:24:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:24:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:24:08] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:24:15] This is snippy 4.6.0
Show full stderr[17:24:15] This is snippy 4.6.0 [17:24:15] Written by Torsten Seemann [17:24:15] Obtained from https://github.com/tseemann/snippy [17:24:15] Detected operating system: linux [17:24:15] Enabling bundled linux tools. [17:24:15] Found bwa - /usr/local/bin/bwa [17:24:15] Found bcftools - /usr/local/bin/bcftools [17:24:15] Found samtools - /usr/local/bin/samtools [17:24:15] Found java - /usr/local/bin/java [17:24:15] Found snpEff - /usr/local/bin/snpEff [17:24:15] Found samclip - /usr/local/bin/samclip [17:24:15] Found seqtk - /usr/local/bin/seqtk [17:24:15] Found parallel - /usr/local/bin/parallel [17:24:15] Found freebayes - /usr/local/bin/freebayes [17:24:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:24:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:24:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:24:15] Found vcfuniq - /usr/local/bin/vcfuniq [17:24:15] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:24:15] Found gzip - /bin/gzip [17:24:15] Found vt - /usr/local/bin/vt [17:24:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:24:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:24:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:24:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:24:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:24:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:24:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:24:15] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:25:18] This is snippy 4.6.0
Show full stderr[17:25:18] This is snippy 4.6.0 [17:25:18] Written by Torsten Seemann [17:25:18] Obtained from https://github.com/tseemann/snippy [17:25:18] Detected operating system: linux [17:25:18] Enabling bundled linux tools. [17:25:18] Found bwa - /usr/local/bin/bwa [17:25:18] Found bcftools - /usr/local/bin/bcftools [17:25:18] Found samtools - /usr/local/bin/samtools [17:25:18] Found java - /usr/local/bin/java [17:25:18] Found snpEff - /usr/local/bin/snpEff [17:25:18] Found samclip - /usr/local/bin/samclip [17:25:18] Found seqtk - /usr/local/bin/seqtk [17:25:18] Found parallel - /usr/local/bin/parallel [17:25:18] Found freebayes - /usr/local/bin/freebayes [17:25:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:25:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:25:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:25:18] Found vcfuniq - /usr/local/bin/vcfuniq [17:25:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:25:18] Found gzip - /bin/gzip [17:25:18] Found vt - /usr/local/bin/vt [17:25:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:25:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:25:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:25:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:25:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:25:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:25:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:25:19] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:25:36] This is snippy 4.6.0
Show full stderr[17:25:36] This is snippy 4.6.0 [17:25:36] Written by Torsten Seemann [17:25:36] Obtained from https://github.com/tseemann/snippy [17:25:36] Detected operating system: linux [17:25:36] Enabling bundled linux tools. [17:25:36] Found bwa - /usr/local/bin/bwa [17:25:36] Found bcftools - /usr/local/bin/bcftools [17:25:36] Found samtools - /usr/local/bin/samtools [17:25:36] Found java - /usr/local/bin/java [17:25:36] Found snpEff - /usr/local/bin/snpEff [17:25:36] Found samclip - /usr/local/bin/samclip [17:25:36] Found seqtk - /usr/local/bin/seqtk [17:25:36] Found parallel - /usr/local/bin/parallel [17:25:36] Found freebayes - /usr/local/bin/freebayes [17:25:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:25:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:25:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:25:36] Found vcfuniq - /usr/local/bin/vcfuniq [17:25:36] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:25:36] Found gzip - /bin/gzip [17:25:36] Found vt - /usr/local/bin/vt [17:25:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:25:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:25:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:25:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:25:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:25:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:25:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:25:37] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:25:51] This is snippy 4.6.0
Show full stderr[17:25:51] This is snippy 4.6.0 [17:25:51] Written by Torsten Seemann [17:25:51] Obtained from https://github.com/tseemann/snippy [17:25:51] Detected operating system: linux [17:25:51] Enabling bundled linux tools. [17:25:51] Found bwa - /usr/local/bin/bwa [17:25:51] Found bcftools - /usr/local/bin/bcftools [17:25:51] Found samtools - /usr/local/bin/samtools [17:25:51] Found java - /usr/local/bin/java [17:25:51] Found snpEff - /usr/local/bin/snpEff [17:25:51] Found samclip - /usr/local/bin/samclip [17:25:51] Found seqtk - /usr/local/bin/seqtk [17:25:51] Found parallel - /usr/local/bin/parallel [17:25:51] Found freebayes - /usr/local/bin/freebayes [17:25:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:25:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:25:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:25:51] Found vcfuniq - /usr/local/bin/vcfuniq [17:25:51] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:25:51] Found gzip - /bin/gzip [17:25:51] Found vt - /usr/local/bin/vt [17:25:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:25:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:25:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:25:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:25:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:25:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:25:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:25:52] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:30:19] This is snippy 4.6.0
Show full stderr[17:30:19] This is snippy 4.6.0 [17:30:19] Written by Torsten Seemann [17:30:19] Obtained from https://github.com/tseemann/snippy [17:30:19] Detected operating system: linux [17:30:19] Enabling bundled linux tools. [17:30:19] Found bwa - /usr/local/bin/bwa [17:30:19] Found bcftools - /usr/local/bin/bcftools [17:30:19] Found samtools - /usr/local/bin/samtools [17:30:19] Found java - /usr/local/bin/java [17:30:19] Found snpEff - /usr/local/bin/snpEff [17:30:19] Found samclip - /usr/local/bin/samclip [17:30:19] Found seqtk - /usr/local/bin/seqtk [17:30:19] Found parallel - /usr/local/bin/parallel [17:30:19] Found freebayes - /usr/local/bin/freebayes [17:30:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:30:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:30:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:30:19] Found vcfuniq - /usr/local/bin/vcfuniq [17:30:19] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:30:19] Found gzip - /bin/gzip [17:30:19] Found vt - /usr/local/bin/vt [17:30:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:30:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:30:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:30:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:30:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:30:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:30:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:30:23] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:27:22] This is snippy 4.6.0
Show full stderr[17:27:22] This is snippy 4.6.0 [17:27:22] Written by Torsten Seemann [17:27:22] Obtained from https://github.com/tseemann/snippy [17:27:22] Detected operating system: linux [17:27:22] Enabling bundled linux tools. [17:27:22] Found bwa - /usr/local/bin/bwa [17:27:22] Found bcftools - /usr/local/bin/bcftools [17:27:22] Found samtools - /usr/local/bin/samtools [17:27:23] Found java - /usr/local/bin/java [17:27:23] Found snpEff - /usr/local/bin/snpEff [17:27:23] Found samclip - /usr/local/bin/samclip [17:27:23] Found seqtk - /usr/local/bin/seqtk [17:27:23] Found parallel - /usr/local/bin/parallel [17:27:23] Found freebayes - /usr/local/bin/freebayes [17:27:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:27:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:27:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:27:23] Found vcfuniq - /usr/local/bin/vcfuniq [17:27:23] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:27:23] Found gzip - /bin/gzip [17:27:23] Found vt - /usr/local/bin/vt [17:27:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:27:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:27:23] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:27:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:27:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:27:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:27:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:27:24] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:27:40] This is snippy 4.6.0
Show full stderr[17:27:40] This is snippy 4.6.0 [17:27:40] Written by Torsten Seemann [17:27:40] Obtained from https://github.com/tseemann/snippy [17:27:40] Detected operating system: linux [17:27:40] Enabling bundled linux tools. [17:27:40] Found bwa - /usr/local/bin/bwa [17:27:40] Found bcftools - /usr/local/bin/bcftools [17:27:40] Found samtools - /usr/local/bin/samtools [17:27:40] Found java - /usr/local/bin/java [17:27:40] Found snpEff - /usr/local/bin/snpEff [17:27:40] Found samclip - /usr/local/bin/samclip [17:27:40] Found seqtk - /usr/local/bin/seqtk [17:27:41] Found parallel - /usr/local/bin/parallel [17:27:41] Found freebayes - /usr/local/bin/freebayes [17:27:41] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:27:41] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:27:41] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:27:41] Found vcfuniq - /usr/local/bin/vcfuniq [17:27:41] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:27:41] Found gzip - /bin/gzip [17:27:41] Found vt - /usr/local/bin/vt [17:27:41] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:27:41] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:27:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:27:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:27:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:27:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:27:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:27:42] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:23:49] This is snippy 4.6.0
Show full stderr[17:23:49] This is snippy 4.6.0 [17:23:49] Written by Torsten Seemann [17:23:49] Obtained from https://github.com/tseemann/snippy [17:23:49] Detected operating system: linux [17:23:49] Enabling bundled linux tools. [17:23:49] Found bwa - /usr/local/bin/bwa [17:23:49] Found bcftools - /usr/local/bin/bcftools [17:23:49] Found samtools - /usr/local/bin/samtools [17:23:49] Found java - /usr/local/bin/java [17:23:49] Found snpEff - /usr/local/bin/snpEff [17:23:49] Found samclip - /usr/local/bin/samclip [17:23:49] Found seqtk - /usr/local/bin/seqtk [17:23:49] Found parallel - /usr/local/bin/parallel [17:23:49] Found freebayes - /usr/local/bin/freebayes [17:23:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:23:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:23:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:23:49] Found vcfuniq - /usr/local/bin/vcfuniq [17:23:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:23:49] Found gzip - /bin/gzip [17:23:49] Found vt - /usr/local/bin/vt [17:23:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:23:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:23:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:23:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:23:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:23:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:23:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:23:50] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:24:16] This is snippy 4.6.0
Show full stderr[17:24:16] This is snippy 4.6.0 [17:24:16] Written by Torsten Seemann [17:24:16] Obtained from https://github.com/tseemann/snippy [17:24:16] Detected operating system: linux [17:24:16] Enabling bundled linux tools. [17:24:16] Found bwa - /usr/local/bin/bwa [17:24:16] Found bcftools - /usr/local/bin/bcftools [17:24:16] Found samtools - /usr/local/bin/samtools [17:24:16] Found java - /usr/local/bin/java [17:24:16] Found snpEff - /usr/local/bin/snpEff [17:24:16] Found samclip - /usr/local/bin/samclip [17:24:16] Found seqtk - /usr/local/bin/seqtk [17:24:16] Found parallel - /usr/local/bin/parallel [17:24:16] Found freebayes - /usr/local/bin/freebayes [17:24:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:24:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:24:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:24:16] Found vcfuniq - /usr/local/bin/vcfuniq [17:24:16] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:24:16] Found gzip - /bin/gzip [17:24:16] Found vt - /usr/local/bin/vt [17:24:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:24:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:24:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:24:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:24:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:24:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:24:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:24:17] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:30:38] This is snippy 4.6.0
Show full stderr[17:30:38] This is snippy 4.6.0 [17:30:38] Written by Torsten Seemann [17:30:38] Obtained from https://github.com/tseemann/snippy [17:30:38] Detected operating system: linux [17:30:38] Enabling bundled linux tools. [17:30:38] Found bwa - /usr/local/bin/bwa [17:30:38] Found bcftools - /usr/local/bin/bcftools [17:30:39] Found samtools - /usr/local/bin/samtools [17:30:39] Found java - /usr/local/bin/java [17:30:39] Found snpEff - /usr/local/bin/snpEff [17:30:39] Found samclip - /usr/local/bin/samclip [17:30:39] Found seqtk - /usr/local/bin/seqtk [17:30:39] Found parallel - /usr/local/bin/parallel [17:30:39] Found freebayes - /usr/local/bin/freebayes [17:30:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:30:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:30:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:30:39] Found vcfuniq - /usr/local/bin/vcfuniq [17:30:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:30:39] Found gzip - /bin/gzip [17:30:39] Found vt - /usr/local/bin/vt [17:30:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:30:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:30:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:30:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:30:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:30:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:30:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:30:40] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:24:36] This is snippy 4.6.0
Show full stderr[17:24:36] This is snippy 4.6.0 [17:24:36] Written by Torsten Seemann [17:24:36] Obtained from https://github.com/tseemann/snippy [17:24:36] Detected operating system: linux [17:24:36] Enabling bundled linux tools. [17:24:36] Found bwa - /usr/local/bin/bwa [17:24:36] Found bcftools - /usr/local/bin/bcftools [17:24:36] Found samtools - /usr/local/bin/samtools [17:24:36] Found java - /usr/local/bin/java [17:24:36] Found snpEff - /usr/local/bin/snpEff [17:24:36] Found samclip - /usr/local/bin/samclip [17:24:36] Found seqtk - /usr/local/bin/seqtk [17:24:36] Found parallel - /usr/local/bin/parallel [17:24:36] Found freebayes - /usr/local/bin/freebayes [17:24:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:24:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:24:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:24:36] Found vcfuniq - /usr/local/bin/vcfuniq [17:24:36] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:24:36] Found gzip - /bin/gzip [17:24:36] Found vt - /usr/local/bin/vt [17:24:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:24:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:24:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:24:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:24:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:24:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:24:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:24:38] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:25:08] This is snippy 4.6.0
Show full stderr[17:25:08] This is snippy 4.6.0 [17:25:08] Written by Torsten Seemann [17:25:08] Obtained from https://github.com/tseemann/snippy [17:25:08] Detected operating system: linux [17:25:08] Enabling bundled linux tools. [17:25:08] Found bwa - /usr/local/bin/bwa [17:25:08] Found bcftools - /usr/local/bin/bcftools [17:25:08] Found samtools - /usr/local/bin/samtools [17:25:08] Found java - /usr/local/bin/java [17:25:08] Found snpEff - /usr/local/bin/snpEff [17:25:08] Found samclip - /usr/local/bin/samclip [17:25:08] Found seqtk - /usr/local/bin/seqtk [17:25:08] Found parallel - /usr/local/bin/parallel [17:25:08] Found freebayes - /usr/local/bin/freebayes [17:25:08] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:25:08] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:25:08] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:25:08] Found vcfuniq - /usr/local/bin/vcfuniq [17:25:08] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:25:08] Found gzip - /bin/gzip [17:25:08] Found vt - /usr/local/bin/vt [17:25:08] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:25:08] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:25:08] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:25:08] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:25:08] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:25:09] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:25:09] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:25:09] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:25:45] This is snippy 4.6.0
Show full stderr[17:25:45] This is snippy 4.6.0 [17:25:45] Written by Torsten Seemann [17:25:45] Obtained from https://github.com/tseemann/snippy [17:25:45] Detected operating system: linux [17:25:45] Enabling bundled linux tools. [17:25:45] Found bwa - /usr/local/bin/bwa [17:25:45] Found bcftools - /usr/local/bin/bcftools [17:25:45] Found samtools - /usr/local/bin/samtools [17:25:45] Found java - /usr/local/bin/java [17:25:45] Found snpEff - /usr/local/bin/snpEff [17:25:45] Found samclip - /usr/local/bin/samclip [17:25:45] Found seqtk - /usr/local/bin/seqtk [17:25:45] Found parallel - /usr/local/bin/parallel [17:25:45] Found freebayes - /usr/local/bin/freebayes [17:25:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:25:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:25:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:25:46] Found vcfuniq - /usr/local/bin/vcfuniq [17:25:46] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:25:46] Found gzip - /bin/gzip [17:25:46] Found vt - /usr/local/bin/vt [17:25:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:25:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:25:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:25:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:25:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:25:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:25:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:25:47] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:25:42] This is snippy 4.6.0
Show full stderr[17:25:42] This is snippy 4.6.0 [17:25:42] Written by Torsten Seemann [17:25:42] Obtained from https://github.com/tseemann/snippy [17:25:42] Detected operating system: linux [17:25:42] Enabling bundled linux tools. [17:25:42] Found bwa - /usr/local/bin/bwa [17:25:42] Found bcftools - /usr/local/bin/bcftools [17:25:42] Found samtools - /usr/local/bin/samtools [17:25:42] Found java - /usr/local/bin/java [17:25:42] Found snpEff - /usr/local/bin/snpEff [17:25:42] Found samclip - /usr/local/bin/samclip [17:25:42] Found seqtk - /usr/local/bin/seqtk [17:25:42] Found parallel - /usr/local/bin/parallel [17:25:42] Found freebayes - /usr/local/bin/freebayes [17:25:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:25:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:25:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:25:42] Found vcfuniq - /usr/local/bin/vcfuniq [17:25:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:25:42] Found gzip - /bin/gzip [17:25:42] Found vt - /usr/local/bin/vt [17:25:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:25:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:25:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:25:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:25:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:25:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:25:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:25:43] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:55:24] This is snippy 4.6.0
Show full stderr[17:55:24] This is snippy 4.6.0 [17:55:24] Written by Torsten Seemann [17:55:24] Obtained from https://github.com/tseemann/snippy [17:55:24] Detected operating system: linux [17:55:24] Enabling bundled linux tools. [17:55:24] Found bwa - /usr/local/bin/bwa [17:55:24] Found bcftools - /usr/local/bin/bcftools [17:55:24] Found samtools - /usr/local/bin/samtools [17:55:24] Found java - /usr/local/bin/java [17:55:24] Found snpEff - /usr/local/bin/snpEff [17:55:24] Found samclip - /usr/local/bin/samclip [17:55:24] Found seqtk - /usr/local/bin/seqtk [17:55:24] Found parallel - /usr/local/bin/parallel [17:55:24] Found freebayes - /usr/local/bin/freebayes [17:55:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:55:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:55:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:55:24] Found vcfuniq - /usr/local/bin/vcfuniq [17:55:24] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:55:24] Found gzip - /bin/gzip [17:55:24] Found vt - /usr/local/bin/vt [17:55:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:55:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:55:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:55:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:55:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:55:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:55:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:55:25] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:58:03] This is snippy 4.6.0
Show full stderr[17:58:03] This is snippy 4.6.0 [17:58:03] Written by Torsten Seemann [17:58:03] Obtained from https://github.com/tseemann/snippy [17:58:03] Detected operating system: linux [17:58:03] Enabling bundled linux tools. [17:58:03] Found bwa - /usr/local/bin/bwa [17:58:03] Found bcftools - /usr/local/bin/bcftools [17:58:04] Found samtools - /usr/local/bin/samtools [17:58:04] Found java - /usr/local/bin/java [17:58:04] Found snpEff - /usr/local/bin/snpEff [17:58:04] Found samclip - /usr/local/bin/samclip [17:58:04] Found seqtk - /usr/local/bin/seqtk [17:58:04] Found parallel - /usr/local/bin/parallel [17:58:04] Found freebayes - /usr/local/bin/freebayes [17:58:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:58:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:58:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:58:04] Found vcfuniq - /usr/local/bin/vcfuniq [17:58:04] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:58:04] Found gzip - /bin/gzip [17:58:04] Found vt - /usr/local/bin/vt [17:58:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:58:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:58:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:58:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:58:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:58:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:58:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:58:05] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:26:09] This is snippy 4.6.0
Show full stderr[17:26:09] This is snippy 4.6.0 [17:26:09] Written by Torsten Seemann [17:26:09] Obtained from https://github.com/tseemann/snippy [17:26:09] Detected operating system: linux [17:26:09] Enabling bundled linux tools. [17:26:09] Found bwa - /usr/local/bin/bwa [17:26:09] Found bcftools - /usr/local/bin/bcftools [17:26:09] Found samtools - /usr/local/bin/samtools [17:26:09] Found java - /usr/local/bin/java [17:26:09] Found snpEff - /usr/local/bin/snpEff [17:26:09] Found samclip - /usr/local/bin/samclip [17:26:09] Found seqtk - /usr/local/bin/seqtk [17:26:09] Found parallel - /usr/local/bin/parallel [17:26:09] Found freebayes - /usr/local/bin/freebayes [17:26:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:26:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:26:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:26:09] Found vcfuniq - /usr/local/bin/vcfuniq [17:26:09] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:26:09] Found gzip - /bin/gzip [17:26:09] Found vt - /usr/local/bin/vt [17:26:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:26:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:26:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:26:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:26:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:26:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:26:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:26:10] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:58:10] This is snippy 4.6.0
Show full stderr[17:58:10] This is snippy 4.6.0 [17:58:10] Written by Torsten Seemann [17:58:10] Obtained from https://github.com/tseemann/snippy [17:58:10] Detected operating system: linux [17:58:10] Enabling bundled linux tools. [17:58:10] Found bwa - /usr/local/bin/bwa [17:58:10] Found bcftools - /usr/local/bin/bcftools [17:58:10] Found samtools - /usr/local/bin/samtools [17:58:10] Found java - /usr/local/bin/java [17:58:10] Found snpEff - /usr/local/bin/snpEff [17:58:10] Found samclip - /usr/local/bin/samclip [17:58:10] Found seqtk - /usr/local/bin/seqtk [17:58:10] Found parallel - /usr/local/bin/parallel [17:58:10] Found freebayes - /usr/local/bin/freebayes [17:58:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:58:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:58:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:58:10] Found vcfuniq - /usr/local/bin/vcfuniq [17:58:10] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:58:10] Found gzip - /bin/gzip [17:58:10] Found vt - /usr/local/bin/vt [17:58:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:58:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:58:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:58:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:58:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:58:12] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:58:12] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:58:12] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:26:36] This is snippy 4.6.0
Show full stderr[17:26:36] This is snippy 4.6.0 [17:26:36] Written by Torsten Seemann [17:26:36] Obtained from https://github.com/tseemann/snippy [17:26:36] Detected operating system: linux [17:26:36] Enabling bundled linux tools. [17:26:36] Found bwa - /usr/local/bin/bwa [17:26:36] Found bcftools - /usr/local/bin/bcftools [17:26:36] Found samtools - /usr/local/bin/samtools [17:26:36] Found java - /usr/local/bin/java [17:26:36] Found snpEff - /usr/local/bin/snpEff [17:26:36] Found samclip - /usr/local/bin/samclip [17:26:36] Found seqtk - /usr/local/bin/seqtk [17:26:36] Found parallel - /usr/local/bin/parallel [17:26:36] Found freebayes - /usr/local/bin/freebayes [17:26:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:26:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:26:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:26:37] Found vcfuniq - /usr/local/bin/vcfuniq [17:26:37] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:26:37] Found gzip - /bin/gzip [17:26:37] Found vt - /usr/local/bin/vt [17:26:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:26:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:26:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:26:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:26:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:26:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:26:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:26:38] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:24:21] This is snippy 4.6.0
Show full stderr[17:24:21] This is snippy 4.6.0 [17:24:21] Written by Torsten Seemann [17:24:21] Obtained from https://github.com/tseemann/snippy [17:24:21] Detected operating system: linux [17:24:21] Enabling bundled linux tools. [17:24:21] Found bwa - /usr/local/bin/bwa [17:24:21] Found bcftools - /usr/local/bin/bcftools [17:24:21] Found samtools - /usr/local/bin/samtools [17:24:21] Found java - /usr/local/bin/java [17:24:21] Found snpEff - /usr/local/bin/snpEff [17:24:21] Found samclip - /usr/local/bin/samclip [17:24:21] Found seqtk - /usr/local/bin/seqtk [17:24:21] Found parallel - /usr/local/bin/parallel [17:24:21] Found freebayes - /usr/local/bin/freebayes [17:24:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:24:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:24:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:24:21] Found vcfuniq - /usr/local/bin/vcfuniq [17:24:21] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:24:21] Found gzip - /bin/gzip [17:24:21] Found vt - /usr/local/bin/vt [17:24:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:24:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:24:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:24:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:24:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:24:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:24:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:24:22] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:24:42] This is snippy 4.6.0
Show full stderr[17:24:42] This is snippy 4.6.0 [17:24:42] Written by Torsten Seemann [17:24:42] Obtained from https://github.com/tseemann/snippy [17:24:42] Detected operating system: linux [17:24:42] Enabling bundled linux tools. [17:24:42] Found bwa - /usr/local/bin/bwa [17:24:42] Found bcftools - /usr/local/bin/bcftools [17:24:42] Found samtools - /usr/local/bin/samtools [17:24:42] Found java - /usr/local/bin/java [17:24:42] Found snpEff - /usr/local/bin/snpEff [17:24:42] Found samclip - /usr/local/bin/samclip [17:24:42] Found seqtk - /usr/local/bin/seqtk [17:24:42] Found parallel - /usr/local/bin/parallel [17:24:42] Found freebayes - /usr/local/bin/freebayes [17:24:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:24:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:24:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:24:42] Found vcfuniq - /usr/local/bin/vcfuniq [17:24:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:24:42] Found gzip - /bin/gzip [17:24:42] Found vt - /usr/local/bin/vt [17:24:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:24:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:24:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:24:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:24:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:24:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:24:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:24:43] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:24:48] This is snippy 4.6.0
Show full stderr[17:24:48] This is snippy 4.6.0 [17:24:48] Written by Torsten Seemann [17:24:48] Obtained from https://github.com/tseemann/snippy [17:24:48] Detected operating system: linux [17:24:48] Enabling bundled linux tools. [17:24:48] Found bwa - /usr/local/bin/bwa [17:24:48] Found bcftools - /usr/local/bin/bcftools [17:24:48] Found samtools - /usr/local/bin/samtools [17:24:48] Found java - /usr/local/bin/java [17:24:48] Found snpEff - /usr/local/bin/snpEff [17:24:48] Found samclip - /usr/local/bin/samclip [17:24:48] Found seqtk - /usr/local/bin/seqtk [17:24:48] Found parallel - /usr/local/bin/parallel [17:24:48] Found freebayes - /usr/local/bin/freebayes [17:24:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:24:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:24:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:24:48] Found vcfuniq - /usr/local/bin/vcfuniq [17:24:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:24:49] Found gzip - /bin/gzip [17:24:49] Found vt - /usr/local/bin/vt [17:24:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:24:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:24:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:24:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:24:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:24:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:24:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:24:50] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:24:57] This is snippy 4.6.0
Show full stderr[17:24:57] This is snippy 4.6.0 [17:24:57] Written by Torsten Seemann [17:24:57] Obtained from https://github.com/tseemann/snippy [17:24:57] Detected operating system: linux [17:24:57] Enabling bundled linux tools. [17:24:57] Found bwa - /usr/local/bin/bwa [17:24:57] Found bcftools - /usr/local/bin/bcftools [17:24:57] Found samtools - /usr/local/bin/samtools [17:24:57] Found java - /usr/local/bin/java [17:24:57] Found snpEff - /usr/local/bin/snpEff [17:24:57] Found samclip - /usr/local/bin/samclip [17:24:57] Found seqtk - /usr/local/bin/seqtk [17:24:57] Found parallel - /usr/local/bin/parallel [17:24:57] Found freebayes - /usr/local/bin/freebayes [17:24:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:24:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:24:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:24:57] Found vcfuniq - /usr/local/bin/vcfuniq [17:24:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:24:57] Found gzip - /bin/gzip [17:24:57] Found vt - /usr/local/bin/vt [17:24:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:24:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:24:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:24:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:24:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:24:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:24:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:24:58] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:36:39] This is snippy 4.6.0
Show full stderr[17:36:39] This is snippy 4.6.0 [17:36:39] Written by Torsten Seemann [17:36:39] Obtained from https://github.com/tseemann/snippy [17:36:39] Detected operating system: linux [17:36:39] Enabling bundled linux tools. [17:36:39] Found bwa - /usr/local/bin/bwa [17:36:39] Found bcftools - /usr/local/bin/bcftools [17:36:39] Found samtools - /usr/local/bin/samtools [17:36:39] Found java - /usr/local/bin/java [17:36:39] Found snpEff - /usr/local/bin/snpEff [17:36:39] Found samclip - /usr/local/bin/samclip [17:36:39] Found seqtk - /usr/local/bin/seqtk [17:36:39] Found parallel - /usr/local/bin/parallel [17:36:39] Found freebayes - /usr/local/bin/freebayes [17:36:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:36:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:36:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:36:39] Found vcfuniq - /usr/local/bin/vcfuniq [17:36:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:36:39] Found gzip - /bin/gzip [17:36:39] Found vt - /usr/local/bin/vt [17:36:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:36:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:36:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:36:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:36:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:36:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:36:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:36:45] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:25:14] This is snippy 4.6.0
Show full stderr[17:25:14] This is snippy 4.6.0 [17:25:14] Written by Torsten Seemann [17:25:14] Obtained from https://github.com/tseemann/snippy [17:25:14] Detected operating system: linux [17:25:14] Enabling bundled linux tools. [17:25:14] Found bwa - /usr/local/bin/bwa [17:25:14] Found bcftools - /usr/local/bin/bcftools [17:25:14] Found samtools - /usr/local/bin/samtools [17:25:14] Found java - /usr/local/bin/java [17:25:14] Found snpEff - /usr/local/bin/snpEff [17:25:14] Found samclip - /usr/local/bin/samclip [17:25:14] Found seqtk - /usr/local/bin/seqtk [17:25:14] Found parallel - /usr/local/bin/parallel [17:25:14] Found freebayes - /usr/local/bin/freebayes [17:25:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:25:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:25:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:25:14] Found vcfuniq - /usr/local/bin/vcfuniq [17:25:14] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:25:14] Found gzip - /bin/gzip [17:25:14] Found vt - /usr/local/bin/vt [17:25:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:25:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:25:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:25:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:25:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:25:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:25:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:25:15] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:42:49] This is snippy 4.6.0
Show full stderr[17:42:49] This is snippy 4.6.0 [17:42:49] Written by Torsten Seemann [17:42:49] Obtained from https://github.com/tseemann/snippy [17:42:49] Detected operating system: linux [17:42:49] Enabling bundled linux tools. [17:42:49] Found bwa - /usr/local/bin/bwa [17:42:49] Found bcftools - /usr/local/bin/bcftools [17:42:49] Found samtools - /usr/local/bin/samtools [17:42:49] Found java - /usr/local/bin/java [17:42:49] Found snpEff - /usr/local/bin/snpEff [17:42:49] Found samclip - /usr/local/bin/samclip [17:42:49] Found seqtk - /usr/local/bin/seqtk [17:42:49] Found parallel - /usr/local/bin/parallel [17:42:49] Found freebayes - /usr/local/bin/freebayes [17:42:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:42:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:42:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:42:49] Found vcfuniq - /usr/local/bin/vcfuniq [17:42:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:42:49] Found gzip - /bin/gzip [17:42:49] Found vt - /usr/local/bin/vt [17:42:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:42:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:42:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:42:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:42:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:42:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:42:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:42:50] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:25:54] This is snippy 4.6.0
Show full stderr[17:25:54] This is snippy 4.6.0 [17:25:54] Written by Torsten Seemann [17:25:54] Obtained from https://github.com/tseemann/snippy [17:25:54] Detected operating system: linux [17:25:54] Enabling bundled linux tools. [17:25:54] Found bwa - /usr/local/bin/bwa [17:25:54] Found bcftools - /usr/local/bin/bcftools [17:25:54] Found samtools - /usr/local/bin/samtools [17:25:54] Found java - /usr/local/bin/java [17:25:54] Found snpEff - /usr/local/bin/snpEff [17:25:54] Found samclip - /usr/local/bin/samclip [17:25:54] Found seqtk - /usr/local/bin/seqtk [17:25:54] Found parallel - /usr/local/bin/parallel [17:25:54] Found freebayes - /usr/local/bin/freebayes [17:25:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:25:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:25:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:25:54] Found vcfuniq - /usr/local/bin/vcfuniq [17:25:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:25:54] Found gzip - /bin/gzip [17:25:54] Found vt - /usr/local/bin/vt [17:25:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:25:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:25:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:25:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:25:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:25:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:25:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:25:54] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:26:07] This is snippy 4.6.0
Show full stderr[17:26:07] This is snippy 4.6.0 [17:26:07] Written by Torsten Seemann [17:26:07] Obtained from https://github.com/tseemann/snippy [17:26:07] Detected operating system: linux [17:26:07] Enabling bundled linux tools. [17:26:07] Found bwa - /usr/local/bin/bwa [17:26:07] Found bcftools - /usr/local/bin/bcftools [17:26:07] Found samtools - /usr/local/bin/samtools [17:26:07] Found java - /usr/local/bin/java [17:26:07] Found snpEff - /usr/local/bin/snpEff [17:26:07] Found samclip - /usr/local/bin/samclip [17:26:07] Found seqtk - /usr/local/bin/seqtk [17:26:07] Found parallel - /usr/local/bin/parallel [17:26:08] Found freebayes - /usr/local/bin/freebayes [17:26:08] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:26:08] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:26:08] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:26:08] Found vcfuniq - /usr/local/bin/vcfuniq [17:26:08] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:26:08] Found gzip - /bin/gzip [17:26:08] Found vt - /usr/local/bin/vt [17:26:08] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:26:08] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:26:08] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:26:08] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:26:08] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:26:09] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:26:09] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:26:09] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:26:15] This is snippy 4.6.0
Show full stderr[17:26:15] This is snippy 4.6.0 [17:26:15] Written by Torsten Seemann [17:26:15] Obtained from https://github.com/tseemann/snippy [17:26:15] Detected operating system: linux [17:26:15] Enabling bundled linux tools. [17:26:15] Found bwa - /usr/local/bin/bwa [17:26:15] Found bcftools - /usr/local/bin/bcftools [17:26:15] Found samtools - /usr/local/bin/samtools [17:26:15] Found java - /usr/local/bin/java [17:26:15] Found snpEff - /usr/local/bin/snpEff [17:26:15] Found samclip - /usr/local/bin/samclip [17:26:16] Found seqtk - /usr/local/bin/seqtk [17:26:16] Found parallel - /usr/local/bin/parallel [17:26:16] Found freebayes - /usr/local/bin/freebayes [17:26:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:26:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:26:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:26:16] Found vcfuniq - /usr/local/bin/vcfuniq [17:26:16] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:26:16] Found gzip - /bin/gzip [17:26:16] Found vt - /usr/local/bin/vt [17:26:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:26:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:26:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:26:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:26:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:26:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:26:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:26:17] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:24:17] This is snippy 4.6.0
Show full stderr[17:24:17] This is snippy 4.6.0 [17:24:17] Written by Torsten Seemann [17:24:17] Obtained from https://github.com/tseemann/snippy [17:24:17] Detected operating system: linux [17:24:17] Enabling bundled linux tools. [17:24:17] Found bwa - /usr/local/bin/bwa [17:24:17] Found bcftools - /usr/local/bin/bcftools [17:24:17] Found samtools - /usr/local/bin/samtools [17:24:17] Found java - /usr/local/bin/java [17:24:17] Found snpEff - /usr/local/bin/snpEff [17:24:17] Found samclip - /usr/local/bin/samclip [17:24:17] Found seqtk - /usr/local/bin/seqtk [17:24:17] Found parallel - /usr/local/bin/parallel [17:24:17] Found freebayes - /usr/local/bin/freebayes [17:24:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:24:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:24:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:24:17] Found vcfuniq - /usr/local/bin/vcfuniq [17:24:17] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:24:17] Found gzip - /bin/gzip [17:24:17] Found vt - /usr/local/bin/vt [17:24:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:24:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:24:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:24:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:24:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:24:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:24:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:24:18] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:24:12] This is snippy 4.6.0
Show full stderr[17:24:12] This is snippy 4.6.0 [17:24:12] Written by Torsten Seemann [17:24:12] Obtained from https://github.com/tseemann/snippy [17:24:12] Detected operating system: linux [17:24:12] Enabling bundled linux tools. [17:24:12] Found bwa - /usr/local/bin/bwa [17:24:12] Found bcftools - /usr/local/bin/bcftools [17:24:12] Found samtools - /usr/local/bin/samtools [17:24:12] Found java - /usr/local/bin/java [17:24:12] Found snpEff - /usr/local/bin/snpEff [17:24:12] Found samclip - /usr/local/bin/samclip [17:24:12] Found seqtk - /usr/local/bin/seqtk [17:24:12] Found parallel - /usr/local/bin/parallel [17:24:12] Found freebayes - /usr/local/bin/freebayes [17:24:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:24:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:24:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:24:12] Found vcfuniq - /usr/local/bin/vcfuniq [17:24:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:24:12] Found gzip - /bin/gzip [17:24:12] Found vt - /usr/local/bin/vt [17:24:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:24:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:24:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:24:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:24:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:24:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:24:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:24:13] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:24:45] This is snippy 4.6.0
Show full stderr[17:24:45] This is snippy 4.6.0 [17:24:45] Written by Torsten Seemann [17:24:45] Obtained from https://github.com/tseemann/snippy [17:24:45] Detected operating system: linux [17:24:45] Enabling bundled linux tools. [17:24:45] Found bwa - /usr/local/bin/bwa [17:24:45] Found bcftools - /usr/local/bin/bcftools [17:24:45] Found samtools - /usr/local/bin/samtools [17:24:45] Found java - /usr/local/bin/java [17:24:45] Found snpEff - /usr/local/bin/snpEff [17:24:45] Found samclip - /usr/local/bin/samclip [17:24:45] Found seqtk - /usr/local/bin/seqtk [17:24:45] Found parallel - /usr/local/bin/parallel [17:24:45] Found freebayes - /usr/local/bin/freebayes [17:24:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:24:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:24:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:24:45] Found vcfuniq - /usr/local/bin/vcfuniq [17:24:45] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:24:45] Found gzip - /bin/gzip [17:24:45] Found vt - /usr/local/bin/vt [17:24:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:24:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:24:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:24:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:24:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:24:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:24:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:24:45] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:24:54] This is snippy 4.6.0
Show full stderr[17:24:54] This is snippy 4.6.0 [17:24:54] Written by Torsten Seemann [17:24:54] Obtained from https://github.com/tseemann/snippy [17:24:54] Detected operating system: linux [17:24:54] Enabling bundled linux tools. [17:24:54] Found bwa - /usr/local/bin/bwa [17:24:54] Found bcftools - /usr/local/bin/bcftools [17:24:54] Found samtools - /usr/local/bin/samtools [17:24:54] Found java - /usr/local/bin/java [17:24:54] Found snpEff - /usr/local/bin/snpEff [17:24:54] Found samclip - /usr/local/bin/samclip [17:24:54] Found seqtk - /usr/local/bin/seqtk [17:24:54] Found parallel - /usr/local/bin/parallel [17:24:54] Found freebayes - /usr/local/bin/freebayes [17:24:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:24:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:24:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:24:54] Found vcfuniq - /usr/local/bin/vcfuniq [17:24:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:24:54] Found gzip - /bin/gzip [17:24:54] Found vt - /usr/local/bin/vt [17:24:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:24:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:24:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:24:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:24:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:24:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:24:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:24:55] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:25:00] This is snippy 4.6.0
Show full stderr[17:25:00] This is snippy 4.6.0 [17:25:00] Written by Torsten Seemann [17:25:00] Obtained from https://github.com/tseemann/snippy [17:25:00] Detected operating system: linux [17:25:00] Enabling bundled linux tools. [17:25:01] Found bwa - /usr/local/bin/bwa [17:25:01] Found bcftools - /usr/local/bin/bcftools [17:25:01] Found samtools - /usr/local/bin/samtools [17:25:01] Found java - /usr/local/bin/java [17:25:01] Found snpEff - /usr/local/bin/snpEff [17:25:01] Found samclip - /usr/local/bin/samclip [17:25:01] Found seqtk - /usr/local/bin/seqtk [17:25:01] Found parallel - /usr/local/bin/parallel [17:25:01] Found freebayes - /usr/local/bin/freebayes [17:25:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:25:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:25:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:25:01] Found vcfuniq - /usr/local/bin/vcfuniq [17:25:01] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:25:01] Found gzip - /bin/gzip [17:25:01] Found vt - /usr/local/bin/vt [17:25:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:25:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:25:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:25:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:25:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:25:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:25:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:25:03] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:25:27] This is snippy 4.6.0
Show full stderr[17:25:27] This is snippy 4.6.0 [17:25:27] Written by Torsten Seemann [17:25:27] Obtained from https://github.com/tseemann/snippy [17:25:27] Detected operating system: linux [17:25:27] Enabling bundled linux tools. [17:25:27] Found bwa - /usr/local/bin/bwa [17:25:27] Found bcftools - /usr/local/bin/bcftools [17:25:27] Found samtools - /usr/local/bin/samtools [17:25:27] Found java - /usr/local/bin/java [17:25:27] Found snpEff - /usr/local/bin/snpEff [17:25:27] Found samclip - /usr/local/bin/samclip [17:25:27] Found seqtk - /usr/local/bin/seqtk [17:25:27] Found parallel - /usr/local/bin/parallel [17:25:27] Found freebayes - /usr/local/bin/freebayes [17:25:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:25:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:25:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:25:27] Found vcfuniq - /usr/local/bin/vcfuniq [17:25:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:25:27] Found gzip - /bin/gzip [17:25:27] Found vt - /usr/local/bin/vt [17:25:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:25:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:25:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:25:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:25:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:25:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:25:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:25:27] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:49:06] This is snippy 4.6.0
Show full stderr[17:49:06] This is snippy 4.6.0 [17:49:06] Written by Torsten Seemann [17:49:06] Obtained from https://github.com/tseemann/snippy [17:49:06] Detected operating system: linux [17:49:06] Enabling bundled linux tools. [17:49:06] Found bwa - /usr/local/bin/bwa [17:49:06] Found bcftools - /usr/local/bin/bcftools [17:49:06] Found samtools - /usr/local/bin/samtools [17:49:07] Found java - /usr/local/bin/java [17:49:07] Found snpEff - /usr/local/bin/snpEff [17:49:07] Found samclip - /usr/local/bin/samclip [17:49:07] Found seqtk - /usr/local/bin/seqtk [17:49:07] Found parallel - /usr/local/bin/parallel [17:49:07] Found freebayes - /usr/local/bin/freebayes [17:49:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:49:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:49:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:49:07] Found vcfuniq - /usr/local/bin/vcfuniq [17:49:07] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:49:07] Found gzip - /bin/gzip [17:49:07] Found vt - /usr/local/bin/vt [17:49:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:49:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:49:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:49:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:49:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:49:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:49:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:49:07] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:49:02] This is snippy 4.6.0
Show full stderr[17:49:02] This is snippy 4.6.0 [17:49:02] Written by Torsten Seemann [17:49:02] Obtained from https://github.com/tseemann/snippy [17:49:02] Detected operating system: linux [17:49:02] Enabling bundled linux tools. [17:49:02] Found bwa - /usr/local/bin/bwa [17:49:02] Found bcftools - /usr/local/bin/bcftools [17:49:02] Found samtools - /usr/local/bin/samtools [17:49:02] Found java - /usr/local/bin/java [17:49:02] Found snpEff - /usr/local/bin/snpEff [17:49:02] Found samclip - /usr/local/bin/samclip [17:49:02] Found seqtk - /usr/local/bin/seqtk [17:49:02] Found parallel - /usr/local/bin/parallel [17:49:02] Found freebayes - /usr/local/bin/freebayes [17:49:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:49:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:49:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:49:02] Found vcfuniq - /usr/local/bin/vcfuniq [17:49:02] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:49:02] Found gzip - /bin/gzip [17:49:02] Found vt - /usr/local/bin/vt [17:49:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:49:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:49:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:49:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:49:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:49:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:49:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:49:04] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:55:03] This is snippy 4.6.0
Show full stderr[17:55:03] This is snippy 4.6.0 [17:55:03] Written by Torsten Seemann [17:55:03] Obtained from https://github.com/tseemann/snippy [17:55:03] Detected operating system: linux [17:55:03] Enabling bundled linux tools. [17:55:03] Found bwa - /usr/local/bin/bwa [17:55:03] Found bcftools - /usr/local/bin/bcftools [17:55:03] Found samtools - /usr/local/bin/samtools [17:55:03] Found java - /usr/local/bin/java [17:55:03] Found snpEff - /usr/local/bin/snpEff [17:55:03] Found samclip - /usr/local/bin/samclip [17:55:03] Found seqtk - /usr/local/bin/seqtk [17:55:03] Found parallel - /usr/local/bin/parallel [17:55:03] Found freebayes - /usr/local/bin/freebayes [17:55:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:55:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:55:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:55:03] Found vcfuniq - /usr/local/bin/vcfuniq [17:55:03] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:55:03] Found gzip - /bin/gzip [17:55:03] Found vt - /usr/local/bin/vt [17:55:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:55:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:55:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:55:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:55:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:55:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:55:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:55:07] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:57:39] This is snippy 4.6.0
Show full stderr[17:57:39] This is snippy 4.6.0 [17:57:39] Written by Torsten Seemann [17:57:39] Obtained from https://github.com/tseemann/snippy [17:57:39] Detected operating system: linux [17:57:39] Enabling bundled linux tools. [17:57:39] Found bwa - /usr/local/bin/bwa [17:57:39] Found bcftools - /usr/local/bin/bcftools [17:57:39] Found samtools - /usr/local/bin/samtools [17:57:39] Found java - /usr/local/bin/java [17:57:39] Found snpEff - /usr/local/bin/snpEff [17:57:39] Found samclip - /usr/local/bin/samclip [17:57:39] Found seqtk - /usr/local/bin/seqtk [17:57:39] Found parallel - /usr/local/bin/parallel [17:57:39] Found freebayes - /usr/local/bin/freebayes [17:57:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:57:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:57:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:57:39] Found vcfuniq - /usr/local/bin/vcfuniq [17:57:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:57:39] Found gzip - /bin/gzip [17:57:39] Found vt - /usr/local/bin/vt [17:57:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:57:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:57:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:57:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:57:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:57:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:57:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:57:40] Please supply a reference FASTA/GBK/EMBL file with --reference
1[18:01:36] This is snippy 4.6.0
Show full stderr[18:01:36] This is snippy 4.6.0 [18:01:36] Written by Torsten Seemann [18:01:36] Obtained from https://github.com/tseemann/snippy [18:01:36] Detected operating system: linux [18:01:36] Enabling bundled linux tools. [18:01:36] Found bwa - /usr/local/bin/bwa [18:01:36] Found bcftools - /usr/local/bin/bcftools [18:01:36] Found samtools - /usr/local/bin/samtools [18:01:36] Found java - /usr/local/bin/java [18:01:36] Found snpEff - /usr/local/bin/snpEff [18:01:36] Found samclip - /usr/local/bin/samclip [18:01:36] Found seqtk - /usr/local/bin/seqtk [18:01:36] Found parallel - /usr/local/bin/parallel [18:01:36] Found freebayes - /usr/local/bin/freebayes [18:01:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [18:01:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [18:01:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [18:01:36] Found vcfuniq - /usr/local/bin/vcfuniq [18:01:36] Found vcffirstheader - /usr/local/bin/vcffirstheader [18:01:36] Found gzip - /bin/gzip [18:01:36] Found vt - /usr/local/bin/vt [18:01:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [18:01:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [18:01:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [18:01:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [18:01:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [18:01:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [18:01:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [18:01:42] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:26:08] This is snippy 4.6.0
Show full stderr[17:26:08] This is snippy 4.6.0 [17:26:08] Written by Torsten Seemann [17:26:08] Obtained from https://github.com/tseemann/snippy [17:26:08] Detected operating system: linux [17:26:08] Enabling bundled linux tools. [17:26:08] Found bwa - /usr/local/bin/bwa [17:26:08] Found bcftools - /usr/local/bin/bcftools [17:26:08] Found samtools - /usr/local/bin/samtools [17:26:08] Found java - /usr/local/bin/java [17:26:08] Found snpEff - /usr/local/bin/snpEff [17:26:08] Found samclip - /usr/local/bin/samclip [17:26:08] Found seqtk - /usr/local/bin/seqtk [17:26:08] Found parallel - /usr/local/bin/parallel [17:26:08] Found freebayes - /usr/local/bin/freebayes [17:26:08] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:26:08] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:26:08] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:26:08] Found vcfuniq - /usr/local/bin/vcfuniq [17:26:08] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:26:08] Found gzip - /bin/gzip [17:26:08] Found vt - /usr/local/bin/vt [17:26:08] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:26:08] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:26:08] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:26:08] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:26:08] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:26:09] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:26:09] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:26:09] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:26:23] This is snippy 4.6.0
Show full stderr[17:26:23] This is snippy 4.6.0 [17:26:23] Written by Torsten Seemann [17:26:23] Obtained from https://github.com/tseemann/snippy [17:26:23] Detected operating system: linux [17:26:23] Enabling bundled linux tools. [17:26:23] Found bwa - /usr/local/bin/bwa [17:26:23] Found bcftools - /usr/local/bin/bcftools [17:26:23] Found samtools - /usr/local/bin/samtools [17:26:23] Found java - /usr/local/bin/java [17:26:23] Found snpEff - /usr/local/bin/snpEff [17:26:23] Found samclip - /usr/local/bin/samclip [17:26:23] Found seqtk - /usr/local/bin/seqtk [17:26:23] Found parallel - /usr/local/bin/parallel [17:26:23] Found freebayes - /usr/local/bin/freebayes [17:26:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:26:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:26:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:26:23] Found vcfuniq - /usr/local/bin/vcfuniq [17:26:23] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:26:23] Found gzip - /bin/gzip [17:26:23] Found vt - /usr/local/bin/vt [17:26:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:26:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:26:23] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:26:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:26:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:26:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:26:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:26:24] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:26:38] This is snippy 4.6.0
Show full stderr[17:26:38] This is snippy 4.6.0 [17:26:38] Written by Torsten Seemann [17:26:38] Obtained from https://github.com/tseemann/snippy [17:26:38] Detected operating system: linux [17:26:38] Enabling bundled linux tools. [17:26:38] Found bwa - /usr/local/bin/bwa [17:26:38] Found bcftools - /usr/local/bin/bcftools [17:26:38] Found samtools - /usr/local/bin/samtools [17:26:38] Found java - /usr/local/bin/java [17:26:38] Found snpEff - /usr/local/bin/snpEff [17:26:38] Found samclip - /usr/local/bin/samclip [17:26:38] Found seqtk - /usr/local/bin/seqtk [17:26:38] Found parallel - /usr/local/bin/parallel [17:26:38] Found freebayes - /usr/local/bin/freebayes [17:26:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:26:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:26:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:26:38] Found vcfuniq - /usr/local/bin/vcfuniq [17:26:38] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:26:38] Found gzip - /bin/gzip [17:26:38] Found vt - /usr/local/bin/vt [17:26:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:26:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:26:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:26:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:26:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:26:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:26:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:26:39] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:26:42] This is snippy 4.6.0
Show full stderr[17:26:42] This is snippy 4.6.0 [17:26:42] Written by Torsten Seemann [17:26:42] Obtained from https://github.com/tseemann/snippy [17:26:42] Detected operating system: linux [17:26:42] Enabling bundled linux tools. [17:26:42] Found bwa - /usr/local/bin/bwa [17:26:42] Found bcftools - /usr/local/bin/bcftools [17:26:42] Found samtools - /usr/local/bin/samtools [17:26:42] Found java - /usr/local/bin/java [17:26:42] Found snpEff - /usr/local/bin/snpEff [17:26:42] Found samclip - /usr/local/bin/samclip [17:26:42] Found seqtk - /usr/local/bin/seqtk [17:26:42] Found parallel - /usr/local/bin/parallel [17:26:42] Found freebayes - /usr/local/bin/freebayes [17:26:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:26:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:26:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:26:42] Found vcfuniq - /usr/local/bin/vcfuniq [17:26:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:26:42] Found gzip - /bin/gzip [17:26:42] Found vt - /usr/local/bin/vt [17:26:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:26:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:26:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:26:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:26:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:26:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:26:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:26:43] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:26:55] This is snippy 4.6.0
Show full stderr[17:26:55] This is snippy 4.6.0 [17:26:55] Written by Torsten Seemann [17:26:55] Obtained from https://github.com/tseemann/snippy [17:26:55] Detected operating system: linux [17:26:55] Enabling bundled linux tools. [17:26:55] Found bwa - /usr/local/bin/bwa [17:26:55] Found bcftools - /usr/local/bin/bcftools [17:26:55] Found samtools - /usr/local/bin/samtools [17:26:55] Found java - /usr/local/bin/java [17:26:55] Found snpEff - /usr/local/bin/snpEff [17:26:56] Found samclip - /usr/local/bin/samclip [17:26:56] Found seqtk - /usr/local/bin/seqtk [17:26:56] Found parallel - /usr/local/bin/parallel [17:26:56] Found freebayes - /usr/local/bin/freebayes [17:26:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:26:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:26:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:26:56] Found vcfuniq - /usr/local/bin/vcfuniq [17:26:56] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:26:56] Found gzip - /bin/gzip [17:26:56] Found vt - /usr/local/bin/vt [17:26:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:26:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:26:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:26:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:26:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:26:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:26:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:26:57] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:27:12] This is snippy 4.6.0
Show full stderr[17:27:12] This is snippy 4.6.0 [17:27:12] Written by Torsten Seemann [17:27:12] Obtained from https://github.com/tseemann/snippy [17:27:12] Detected operating system: linux [17:27:12] Enabling bundled linux tools. [17:27:12] Found bwa - /usr/local/bin/bwa [17:27:12] Found bcftools - /usr/local/bin/bcftools [17:27:12] Found samtools - /usr/local/bin/samtools [17:27:12] Found java - /usr/local/bin/java [17:27:12] Found snpEff - /usr/local/bin/snpEff [17:27:12] Found samclip - /usr/local/bin/samclip [17:27:12] Found seqtk - /usr/local/bin/seqtk [17:27:12] Found parallel - /usr/local/bin/parallel [17:27:12] Found freebayes - /usr/local/bin/freebayes [17:27:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:27:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:27:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:27:12] Found vcfuniq - /usr/local/bin/vcfuniq [17:27:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:27:12] Found gzip - /bin/gzip [17:27:12] Found vt - /usr/local/bin/vt [17:27:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:27:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:27:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:27:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:27:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:27:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:27:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:27:13] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:28:14] This is snippy 4.6.0
Show full stderr[17:28:14] This is snippy 4.6.0 [17:28:14] Written by Torsten Seemann [17:28:14] Obtained from https://github.com/tseemann/snippy [17:28:14] Detected operating system: linux [17:28:14] Enabling bundled linux tools. [17:28:14] Found bwa - /usr/local/bin/bwa [17:28:14] Found bcftools - /usr/local/bin/bcftools [17:28:14] Found samtools - /usr/local/bin/samtools [17:28:14] Found java - /usr/local/bin/java [17:28:14] Found snpEff - /usr/local/bin/snpEff [17:28:14] Found samclip - /usr/local/bin/samclip [17:28:14] Found seqtk - /usr/local/bin/seqtk [17:28:14] Found parallel - /usr/local/bin/parallel [17:28:14] Found freebayes - /usr/local/bin/freebayes [17:28:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:28:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:28:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:28:14] Found vcfuniq - /usr/local/bin/vcfuniq [17:28:14] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:28:14] Found gzip - /bin/gzip [17:28:14] Found vt - /usr/local/bin/vt [17:28:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:28:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:28:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:28:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:28:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:28:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:28:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:28:15] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:28:26] This is snippy 4.6.0
Show full stderr[17:28:26] This is snippy 4.6.0 [17:28:26] Written by Torsten Seemann [17:28:26] Obtained from https://github.com/tseemann/snippy [17:28:26] Detected operating system: linux [17:28:26] Enabling bundled linux tools. [17:28:26] Found bwa - /usr/local/bin/bwa [17:28:26] Found bcftools - /usr/local/bin/bcftools [17:28:26] Found samtools - /usr/local/bin/samtools [17:28:26] Found java - /usr/local/bin/java [17:28:26] Found snpEff - /usr/local/bin/snpEff [17:28:26] Found samclip - /usr/local/bin/samclip [17:28:26] Found seqtk - /usr/local/bin/seqtk [17:28:26] Found parallel - /usr/local/bin/parallel [17:28:26] Found freebayes - /usr/local/bin/freebayes [17:28:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:28:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:28:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:28:27] Found vcfuniq - /usr/local/bin/vcfuniq [17:28:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:28:27] Found gzip - /bin/gzip [17:28:27] Found vt - /usr/local/bin/vt [17:28:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:28:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:28:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:28:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:28:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:28:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:28:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:28:28] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:28:30] This is snippy 4.6.0
Show full stderr[17:28:30] This is snippy 4.6.0 [17:28:30] Written by Torsten Seemann [17:28:30] Obtained from https://github.com/tseemann/snippy [17:28:30] Detected operating system: linux [17:28:30] Enabling bundled linux tools. [17:28:30] Found bwa - /usr/local/bin/bwa [17:28:30] Found bcftools - /usr/local/bin/bcftools [17:28:30] Found samtools - /usr/local/bin/samtools [17:28:30] Found java - /usr/local/bin/java [17:28:30] Found snpEff - /usr/local/bin/snpEff [17:28:30] Found samclip - /usr/local/bin/samclip [17:28:30] Found seqtk - /usr/local/bin/seqtk [17:28:30] Found parallel - /usr/local/bin/parallel [17:28:30] Found freebayes - /usr/local/bin/freebayes [17:28:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:28:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:28:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:28:30] Found vcfuniq - /usr/local/bin/vcfuniq [17:28:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:28:30] Found gzip - /bin/gzip [17:28:30] Found vt - /usr/local/bin/vt [17:28:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:28:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:28:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:28:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:28:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:28:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:28:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:28:31] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:29:19] This is snippy 4.6.0
Show full stderr[17:29:19] This is snippy 4.6.0 [17:29:19] Written by Torsten Seemann [17:29:19] Obtained from https://github.com/tseemann/snippy [17:29:19] Detected operating system: linux [17:29:19] Enabling bundled linux tools. [17:29:19] Found bwa - /usr/local/bin/bwa [17:29:19] Found bcftools - /usr/local/bin/bcftools [17:29:19] Found samtools - /usr/local/bin/samtools [17:29:19] Found java - /usr/local/bin/java [17:29:19] Found snpEff - /usr/local/bin/snpEff [17:29:19] Found samclip - /usr/local/bin/samclip [17:29:19] Found seqtk - /usr/local/bin/seqtk [17:29:19] Found parallel - /usr/local/bin/parallel [17:29:19] Found freebayes - /usr/local/bin/freebayes [17:29:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:29:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:29:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:29:19] Found vcfuniq - /usr/local/bin/vcfuniq [17:29:19] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:29:19] Found gzip - /bin/gzip [17:29:19] Found vt - /usr/local/bin/vt [17:29:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:29:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:29:20] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:29:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:29:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:29:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:29:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:29:21] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:29:44] This is snippy 4.6.0
Show full stderr[17:29:44] This is snippy 4.6.0 [17:29:44] Written by Torsten Seemann [17:29:44] Obtained from https://github.com/tseemann/snippy [17:29:44] Detected operating system: linux [17:29:44] Enabling bundled linux tools. [17:29:44] Found bwa - /usr/local/bin/bwa [17:29:44] Found bcftools - /usr/local/bin/bcftools [17:29:44] Found samtools - /usr/local/bin/samtools [17:29:44] Found java - /usr/local/bin/java [17:29:44] Found snpEff - /usr/local/bin/snpEff [17:29:44] Found samclip - /usr/local/bin/samclip [17:29:44] Found seqtk - /usr/local/bin/seqtk [17:29:44] Found parallel - /usr/local/bin/parallel [17:29:44] Found freebayes - /usr/local/bin/freebayes [17:29:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:29:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:29:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:29:44] Found vcfuniq - /usr/local/bin/vcfuniq [17:29:44] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:29:44] Found gzip - /bin/gzip [17:29:44] Found vt - /usr/local/bin/vt [17:29:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:29:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:29:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:29:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:29:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:29:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:29:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:29:46] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:29:45] This is snippy 4.6.0
Show full stderr[17:29:45] This is snippy 4.6.0 [17:29:45] Written by Torsten Seemann [17:29:45] Obtained from https://github.com/tseemann/snippy [17:29:45] Detected operating system: linux [17:29:45] Enabling bundled linux tools. [17:29:46] Found bwa - /usr/local/bin/bwa [17:29:46] Found bcftools - /usr/local/bin/bcftools [17:29:46] Found samtools - /usr/local/bin/samtools [17:29:46] Found java - /usr/local/bin/java [17:29:46] Found snpEff - /usr/local/bin/snpEff [17:29:46] Found samclip - /usr/local/bin/samclip [17:29:46] Found seqtk - /usr/local/bin/seqtk [17:29:46] Found parallel - /usr/local/bin/parallel [17:29:46] Found freebayes - /usr/local/bin/freebayes [17:29:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:29:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:29:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:29:46] Found vcfuniq - /usr/local/bin/vcfuniq [17:29:46] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:29:46] Found gzip - /bin/gzip [17:29:46] Found vt - /usr/local/bin/vt [17:29:46] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:29:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:29:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:29:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:29:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:29:47] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:29:47] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:29:47] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:30:01] This is snippy 4.6.0
Show full stderr[17:30:01] This is snippy 4.6.0 [17:30:01] Written by Torsten Seemann [17:30:01] Obtained from https://github.com/tseemann/snippy [17:30:01] Detected operating system: linux [17:30:01] Enabling bundled linux tools. [17:30:01] Found bwa - /usr/local/bin/bwa [17:30:01] Found bcftools - /usr/local/bin/bcftools [17:30:01] Found samtools - /usr/local/bin/samtools [17:30:01] Found java - /usr/local/bin/java [17:30:01] Found snpEff - /usr/local/bin/snpEff [17:30:01] Found samclip - /usr/local/bin/samclip [17:30:01] Found seqtk - /usr/local/bin/seqtk [17:30:01] Found parallel - /usr/local/bin/parallel [17:30:02] Found freebayes - /usr/local/bin/freebayes [17:30:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:30:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:30:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:30:02] Found vcfuniq - /usr/local/bin/vcfuniq [17:30:02] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:30:02] Found gzip - /bin/gzip [17:30:02] Found vt - /usr/local/bin/vt [17:30:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:30:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:30:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:30:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:30:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:30:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:30:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:30:03] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:30:07] This is snippy 4.6.0
Show full stderr[17:30:07] This is snippy 4.6.0 [17:30:07] Written by Torsten Seemann [17:30:07] Obtained from https://github.com/tseemann/snippy [17:30:07] Detected operating system: linux [17:30:07] Enabling bundled linux tools. [17:30:07] Found bwa - /usr/local/bin/bwa [17:30:07] Found bcftools - /usr/local/bin/bcftools [17:30:08] Found samtools - /usr/local/bin/samtools [17:30:08] Found java - /usr/local/bin/java [17:30:08] Found snpEff - /usr/local/bin/snpEff [17:30:08] Found samclip - /usr/local/bin/samclip [17:30:08] Found seqtk - /usr/local/bin/seqtk [17:30:08] Found parallel - /usr/local/bin/parallel [17:30:08] Found freebayes - /usr/local/bin/freebayes [17:30:08] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:30:08] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:30:08] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:30:08] Found vcfuniq - /usr/local/bin/vcfuniq [17:30:08] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:30:08] Found gzip - /bin/gzip [17:30:08] Found vt - /usr/local/bin/vt [17:30:08] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:30:08] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:30:08] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:30:08] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:30:08] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:30:09] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:30:09] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:30:09] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:30:45] This is snippy 4.6.0
Show full stderr[17:30:45] This is snippy 4.6.0 [17:30:45] Written by Torsten Seemann [17:30:45] Obtained from https://github.com/tseemann/snippy [17:30:45] Detected operating system: linux [17:30:45] Enabling bundled linux tools. [17:30:45] Found bwa - /usr/local/bin/bwa [17:30:45] Found bcftools - /usr/local/bin/bcftools [17:30:45] Found samtools - /usr/local/bin/samtools [17:30:45] Found java - /usr/local/bin/java [17:30:45] Found snpEff - /usr/local/bin/snpEff [17:30:45] Found samclip - /usr/local/bin/samclip [17:30:45] Found seqtk - /usr/local/bin/seqtk [17:30:45] Found parallel - /usr/local/bin/parallel [17:30:45] Found freebayes - /usr/local/bin/freebayes [17:30:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:30:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:30:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:30:45] Found vcfuniq - /usr/local/bin/vcfuniq [17:30:45] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:30:45] Found gzip - /bin/gzip [17:30:45] Found vt - /usr/local/bin/vt [17:30:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:30:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:30:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:30:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:30:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:30:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:30:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:30:46] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:27:58] This is snippy 4.6.0
Show full stderr[17:27:58] This is snippy 4.6.0 [17:27:58] Written by Torsten Seemann [17:27:58] Obtained from https://github.com/tseemann/snippy [17:27:58] Detected operating system: linux [17:27:58] Enabling bundled linux tools. [17:27:58] Found bwa - /usr/local/bin/bwa [17:27:58] Found bcftools - /usr/local/bin/bcftools [17:27:58] Found samtools - /usr/local/bin/samtools [17:27:58] Found java - /usr/local/bin/java [17:27:58] Found snpEff - /usr/local/bin/snpEff [17:27:59] Found samclip - /usr/local/bin/samclip [17:27:59] Found seqtk - /usr/local/bin/seqtk [17:27:59] Found parallel - /usr/local/bin/parallel [17:27:59] Found freebayes - /usr/local/bin/freebayes [17:27:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:27:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:27:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:27:59] Found vcfuniq - /usr/local/bin/vcfuniq [17:27:59] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:27:59] Found gzip - /bin/gzip [17:27:59] Found vt - /usr/local/bin/vt [17:27:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:27:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:27:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:27:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:27:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:28:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:28:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:28:00] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:28:08] This is snippy 4.6.0
Show full stderr[17:28:08] This is snippy 4.6.0 [17:28:08] Written by Torsten Seemann [17:28:08] Obtained from https://github.com/tseemann/snippy [17:28:08] Detected operating system: linux [17:28:08] Enabling bundled linux tools. [17:28:08] Found bwa - /usr/local/bin/bwa [17:28:08] Found bcftools - /usr/local/bin/bcftools [17:28:08] Found samtools - /usr/local/bin/samtools [17:28:08] Found java - /usr/local/bin/java [17:28:08] Found snpEff - /usr/local/bin/snpEff [17:28:08] Found samclip - /usr/local/bin/samclip [17:28:08] Found seqtk - /usr/local/bin/seqtk [17:28:08] Found parallel - /usr/local/bin/parallel [17:28:08] Found freebayes - /usr/local/bin/freebayes [17:28:08] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:28:08] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:28:08] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:28:08] Found vcfuniq - /usr/local/bin/vcfuniq [17:28:08] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:28:08] Found gzip - /bin/gzip [17:28:08] Found vt - /usr/local/bin/vt [17:28:08] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:28:08] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:28:08] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:28:08] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:28:08] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:28:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:28:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:28:08] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:28:02] This is snippy 4.6.0
Show full stderr[17:28:02] This is snippy 4.6.0 [17:28:02] Written by Torsten Seemann [17:28:02] Obtained from https://github.com/tseemann/snippy [17:28:02] Detected operating system: linux [17:28:02] Enabling bundled linux tools. [17:28:02] Found bwa - /usr/local/bin/bwa [17:28:02] Found bcftools - /usr/local/bin/bcftools [17:28:02] Found samtools - /usr/local/bin/samtools [17:28:02] Found java - /usr/local/bin/java [17:28:02] Found snpEff - /usr/local/bin/snpEff [17:28:02] Found samclip - /usr/local/bin/samclip [17:28:02] Found seqtk - /usr/local/bin/seqtk [17:28:02] Found parallel - /usr/local/bin/parallel [17:28:02] Found freebayes - /usr/local/bin/freebayes [17:28:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:28:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:28:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:28:02] Found vcfuniq - /usr/local/bin/vcfuniq [17:28:02] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:28:02] Found gzip - /bin/gzip [17:28:02] Found vt - /usr/local/bin/vt [17:28:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:28:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:28:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:28:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:28:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:28:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:28:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:28:03] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:28:15] This is snippy 4.6.0
Show full stderr[17:28:15] This is snippy 4.6.0 [17:28:15] Written by Torsten Seemann [17:28:15] Obtained from https://github.com/tseemann/snippy [17:28:15] Detected operating system: linux [17:28:15] Enabling bundled linux tools. [17:28:15] Found bwa - /usr/local/bin/bwa [17:28:15] Found bcftools - /usr/local/bin/bcftools [17:28:15] Found samtools - /usr/local/bin/samtools [17:28:15] Found java - /usr/local/bin/java [17:28:15] Found snpEff - /usr/local/bin/snpEff [17:28:15] Found samclip - /usr/local/bin/samclip [17:28:15] Found seqtk - /usr/local/bin/seqtk [17:28:15] Found parallel - /usr/local/bin/parallel [17:28:15] Found freebayes - /usr/local/bin/freebayes [17:28:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:28:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:28:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:28:15] Found vcfuniq - /usr/local/bin/vcfuniq [17:28:15] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:28:16] Found gzip - /bin/gzip [17:28:16] Found vt - /usr/local/bin/vt [17:28:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:28:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:28:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:28:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:28:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:28:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:28:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:28:17] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:28:33] This is snippy 4.6.0
Show full stderr[17:28:33] This is snippy 4.6.0 [17:28:33] Written by Torsten Seemann [17:28:33] Obtained from https://github.com/tseemann/snippy [17:28:33] Detected operating system: linux [17:28:33] Enabling bundled linux tools. [17:28:33] Found bwa - /usr/local/bin/bwa [17:28:33] Found bcftools - /usr/local/bin/bcftools [17:28:33] Found samtools - /usr/local/bin/samtools [17:28:33] Found java - /usr/local/bin/java [17:28:33] Found snpEff - /usr/local/bin/snpEff [17:28:33] Found samclip - /usr/local/bin/samclip [17:28:33] Found seqtk - /usr/local/bin/seqtk [17:28:33] Found parallel - /usr/local/bin/parallel [17:28:33] Found freebayes - /usr/local/bin/freebayes [17:28:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:28:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:28:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:28:33] Found vcfuniq - /usr/local/bin/vcfuniq [17:28:33] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:28:33] Found gzip - /bin/gzip [17:28:33] Found vt - /usr/local/bin/vt [17:28:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:28:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:28:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:28:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:28:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:28:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:28:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:28:34] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:29:03] This is snippy 4.6.0
Show full stderr[17:29:03] This is snippy 4.6.0 [17:29:03] Written by Torsten Seemann [17:29:03] Obtained from https://github.com/tseemann/snippy [17:29:03] Detected operating system: linux [17:29:03] Enabling bundled linux tools. [17:29:03] Found bwa - /usr/local/bin/bwa [17:29:03] Found bcftools - /usr/local/bin/bcftools [17:29:03] Found samtools - /usr/local/bin/samtools [17:29:03] Found java - /usr/local/bin/java [17:29:04] Found snpEff - /usr/local/bin/snpEff [17:29:04] Found samclip - /usr/local/bin/samclip [17:29:04] Found seqtk - /usr/local/bin/seqtk [17:29:04] Found parallel - /usr/local/bin/parallel [17:29:04] Found freebayes - /usr/local/bin/freebayes [17:29:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:29:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:29:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:29:04] Found vcfuniq - /usr/local/bin/vcfuniq [17:29:04] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:29:04] Found gzip - /bin/gzip [17:29:04] Found vt - /usr/local/bin/vt [17:29:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:29:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:29:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:29:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:29:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:29:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:29:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:29:04] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:28:42] This is snippy 4.6.0
Show full stderr[17:28:42] This is snippy 4.6.0 [17:28:42] Written by Torsten Seemann [17:28:42] Obtained from https://github.com/tseemann/snippy [17:28:42] Detected operating system: linux [17:28:42] Enabling bundled linux tools. [17:28:42] Found bwa - /usr/local/bin/bwa [17:28:42] Found bcftools - /usr/local/bin/bcftools [17:28:42] Found samtools - /usr/local/bin/samtools [17:28:42] Found java - /usr/local/bin/java [17:28:42] Found snpEff - /usr/local/bin/snpEff [17:28:42] Found samclip - /usr/local/bin/samclip [17:28:43] Found seqtk - /usr/local/bin/seqtk [17:28:43] Found parallel - /usr/local/bin/parallel [17:28:43] Found freebayes - /usr/local/bin/freebayes [17:28:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:28:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:28:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:28:43] Found vcfuniq - /usr/local/bin/vcfuniq [17:28:43] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:28:43] Found gzip - /bin/gzip [17:28:43] Found vt - /usr/local/bin/vt [17:28:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:28:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:28:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:28:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:28:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:28:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:28:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:28:44] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:29:13] This is snippy 4.6.0
Show full stderr[17:29:13] This is snippy 4.6.0 [17:29:13] Written by Torsten Seemann [17:29:13] Obtained from https://github.com/tseemann/snippy [17:29:13] Detected operating system: linux [17:29:13] Enabling bundled linux tools. [17:29:14] Found bwa - /usr/local/bin/bwa [17:29:14] Found bcftools - /usr/local/bin/bcftools [17:29:14] Found samtools - /usr/local/bin/samtools [17:29:14] Found java - /usr/local/bin/java [17:29:14] Found snpEff - /usr/local/bin/snpEff [17:29:14] Found samclip - /usr/local/bin/samclip [17:29:14] Found seqtk - /usr/local/bin/seqtk [17:29:14] Found parallel - /usr/local/bin/parallel [17:29:14] Found freebayes - /usr/local/bin/freebayes [17:29:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:29:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:29:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:29:14] Found vcfuniq - /usr/local/bin/vcfuniq [17:29:14] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:29:14] Found gzip - /bin/gzip [17:29:14] Found vt - /usr/local/bin/vt [17:29:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:29:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:29:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:29:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:29:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:29:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:29:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:29:15] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:30:05] This is snippy 4.6.0
Show full stderr[17:30:05] This is snippy 4.6.0 [17:30:05] Written by Torsten Seemann [17:30:05] Obtained from https://github.com/tseemann/snippy [17:30:05] Detected operating system: linux [17:30:05] Enabling bundled linux tools. [17:30:05] Found bwa - /usr/local/bin/bwa [17:30:05] Found bcftools - /usr/local/bin/bcftools [17:30:05] Found samtools - /usr/local/bin/samtools [17:30:05] Found java - /usr/local/bin/java [17:30:05] Found snpEff - /usr/local/bin/snpEff [17:30:05] Found samclip - /usr/local/bin/samclip [17:30:05] Found seqtk - /usr/local/bin/seqtk [17:30:05] Found parallel - /usr/local/bin/parallel [17:30:05] Found freebayes - /usr/local/bin/freebayes [17:30:05] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:30:05] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:30:05] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:30:05] Found vcfuniq - /usr/local/bin/vcfuniq [17:30:05] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:30:05] Found gzip - /bin/gzip [17:30:05] Found vt - /usr/local/bin/vt [17:30:05] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:30:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:30:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:30:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:30:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:30:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:30:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:30:06] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:30:10] This is snippy 4.6.0
Show full stderr[17:30:10] This is snippy 4.6.0 [17:30:10] Written by Torsten Seemann [17:30:10] Obtained from https://github.com/tseemann/snippy [17:30:10] Detected operating system: linux [17:30:10] Enabling bundled linux tools. [17:30:11] Found bwa - /usr/local/bin/bwa [17:30:11] Found bcftools - /usr/local/bin/bcftools [17:30:11] Found samtools - /usr/local/bin/samtools [17:30:11] Found java - /usr/local/bin/java [17:30:11] Found snpEff - /usr/local/bin/snpEff [17:30:11] Found samclip - /usr/local/bin/samclip [17:30:11] Found seqtk - /usr/local/bin/seqtk [17:30:11] Found parallel - /usr/local/bin/parallel [17:30:11] Found freebayes - /usr/local/bin/freebayes [17:30:11] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:30:11] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:30:11] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:30:11] Found vcfuniq - /usr/local/bin/vcfuniq [17:30:11] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:30:11] Found gzip - /bin/gzip [17:30:11] Found vt - /usr/local/bin/vt [17:30:11] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:30:11] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:30:11] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:30:11] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:30:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:30:12] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:30:12] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:30:12] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:30:54] This is snippy 4.6.0
Show full stderr[17:30:54] This is snippy 4.6.0 [17:30:54] Written by Torsten Seemann [17:30:54] Obtained from https://github.com/tseemann/snippy [17:30:54] Detected operating system: linux [17:30:54] Enabling bundled linux tools. [17:30:54] Found bwa - /usr/local/bin/bwa [17:30:54] Found bcftools - /usr/local/bin/bcftools [17:30:54] Found samtools - /usr/local/bin/samtools [17:30:54] Found java - /usr/local/bin/java [17:30:54] Found snpEff - /usr/local/bin/snpEff [17:30:54] Found samclip - /usr/local/bin/samclip [17:30:54] Found seqtk - /usr/local/bin/seqtk [17:30:54] Found parallel - /usr/local/bin/parallel [17:30:54] Found freebayes - /usr/local/bin/freebayes [17:30:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:30:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:30:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:30:54] Found vcfuniq - /usr/local/bin/vcfuniq [17:30:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:30:54] Found gzip - /bin/gzip [17:30:54] Found vt - /usr/local/bin/vt [17:30:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:30:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:30:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:30:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:30:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:30:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:30:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:30:55] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:26:41] This is snippy 4.6.0
Show full stderr[17:26:41] This is snippy 4.6.0 [17:26:41] Written by Torsten Seemann [17:26:41] Obtained from https://github.com/tseemann/snippy [17:26:41] Detected operating system: linux [17:26:41] Enabling bundled linux tools. [17:26:41] Found bwa - /usr/local/bin/bwa [17:26:41] Found bcftools - /usr/local/bin/bcftools [17:26:41] Found samtools - /usr/local/bin/samtools [17:26:41] Found java - /usr/local/bin/java [17:26:41] Found snpEff - /usr/local/bin/snpEff [17:26:41] Found samclip - /usr/local/bin/samclip [17:26:41] Found seqtk - /usr/local/bin/seqtk [17:26:41] Found parallel - /usr/local/bin/parallel [17:26:42] Found freebayes - /usr/local/bin/freebayes [17:26:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:26:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:26:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:26:42] Found vcfuniq - /usr/local/bin/vcfuniq [17:26:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:26:42] Found gzip - /bin/gzip [17:26:42] Found vt - /usr/local/bin/vt [17:26:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:26:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:26:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:26:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:26:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:26:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:26:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:26:43] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:26:52] This is snippy 4.6.0
Show full stderr[17:26:52] This is snippy 4.6.0 [17:26:52] Written by Torsten Seemann [17:26:52] Obtained from https://github.com/tseemann/snippy [17:26:52] Detected operating system: linux [17:26:52] Enabling bundled linux tools. [17:26:52] Found bwa - /usr/local/bin/bwa [17:26:52] Found bcftools - /usr/local/bin/bcftools [17:26:52] Found samtools - /usr/local/bin/samtools [17:26:52] Found java - /usr/local/bin/java [17:26:52] Found snpEff - /usr/local/bin/snpEff [17:26:52] Found samclip - /usr/local/bin/samclip [17:26:52] Found seqtk - /usr/local/bin/seqtk [17:26:52] Found parallel - /usr/local/bin/parallel [17:26:52] Found freebayes - /usr/local/bin/freebayes [17:26:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:26:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:26:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:26:52] Found vcfuniq - /usr/local/bin/vcfuniq [17:26:52] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:26:52] Found gzip - /bin/gzip [17:26:52] Found vt - /usr/local/bin/vt [17:26:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:26:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:26:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:26:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:26:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:26:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:26:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:26:53] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:27:06] This is snippy 4.6.0
Show full stderr[17:27:06] This is snippy 4.6.0 [17:27:06] Written by Torsten Seemann [17:27:06] Obtained from https://github.com/tseemann/snippy [17:27:06] Detected operating system: linux [17:27:06] Enabling bundled linux tools. [17:27:06] Found bwa - /usr/local/bin/bwa [17:27:06] Found bcftools - /usr/local/bin/bcftools [17:27:06] Found samtools - /usr/local/bin/samtools [17:27:06] Found java - /usr/local/bin/java [17:27:06] Found snpEff - /usr/local/bin/snpEff [17:27:06] Found samclip - /usr/local/bin/samclip [17:27:06] Found seqtk - /usr/local/bin/seqtk [17:27:06] Found parallel - /usr/local/bin/parallel [17:27:06] Found freebayes - /usr/local/bin/freebayes [17:27:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:27:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:27:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:27:06] Found vcfuniq - /usr/local/bin/vcfuniq [17:27:06] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:27:06] Found gzip - /bin/gzip [17:27:06] Found vt - /usr/local/bin/vt [17:27:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:27:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:27:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:27:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:27:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:27:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:27:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:27:07] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:27:09] This is snippy 4.6.0
Show full stderr[17:27:09] This is snippy 4.6.0 [17:27:09] Written by Torsten Seemann [17:27:09] Obtained from https://github.com/tseemann/snippy [17:27:09] Detected operating system: linux [17:27:09] Enabling bundled linux tools. [17:27:09] Found bwa - /usr/local/bin/bwa [17:27:09] Found bcftools - /usr/local/bin/bcftools [17:27:09] Found samtools - /usr/local/bin/samtools [17:27:09] Found java - /usr/local/bin/java [17:27:09] Found snpEff - /usr/local/bin/snpEff [17:27:09] Found samclip - /usr/local/bin/samclip [17:27:09] Found seqtk - /usr/local/bin/seqtk [17:27:09] Found parallel - /usr/local/bin/parallel [17:27:09] Found freebayes - /usr/local/bin/freebayes [17:27:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:27:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:27:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:27:09] Found vcfuniq - /usr/local/bin/vcfuniq [17:27:09] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:27:09] Found gzip - /bin/gzip [17:27:09] Found vt - /usr/local/bin/vt [17:27:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:27:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:27:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:27:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:27:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:27:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:27:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:27:10] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:27:37] This is snippy 4.6.0
Show full stderr[17:27:37] This is snippy 4.6.0 [17:27:37] Written by Torsten Seemann [17:27:37] Obtained from https://github.com/tseemann/snippy [17:27:37] Detected operating system: linux [17:27:37] Enabling bundled linux tools. [17:27:37] Found bwa - /usr/local/bin/bwa [17:27:37] Found bcftools - /usr/local/bin/bcftools [17:27:37] Found samtools - /usr/local/bin/samtools [17:27:37] Found java - /usr/local/bin/java [17:27:37] Found snpEff - /usr/local/bin/snpEff [17:27:37] Found samclip - /usr/local/bin/samclip [17:27:37] Found seqtk - /usr/local/bin/seqtk [17:27:37] Found parallel - /usr/local/bin/parallel [17:27:37] Found freebayes - /usr/local/bin/freebayes [17:27:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:27:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:27:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:27:37] Found vcfuniq - /usr/local/bin/vcfuniq [17:27:37] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:27:37] Found gzip - /bin/gzip [17:27:37] Found vt - /usr/local/bin/vt [17:27:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:27:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:27:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:27:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:27:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:27:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:27:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:27:38] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:27:39] This is snippy 4.6.0
Show full stderr[17:27:39] This is snippy 4.6.0 [17:27:39] Written by Torsten Seemann [17:27:39] Obtained from https://github.com/tseemann/snippy [17:27:39] Detected operating system: linux [17:27:39] Enabling bundled linux tools. [17:27:39] Found bwa - /usr/local/bin/bwa [17:27:39] Found bcftools - /usr/local/bin/bcftools [17:27:39] Found samtools - /usr/local/bin/samtools [17:27:39] Found java - /usr/local/bin/java [17:27:39] Found snpEff - /usr/local/bin/snpEff [17:27:39] Found samclip - /usr/local/bin/samclip [17:27:39] Found seqtk - /usr/local/bin/seqtk [17:27:39] Found parallel - /usr/local/bin/parallel [17:27:39] Found freebayes - /usr/local/bin/freebayes [17:27:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:27:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:27:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:27:39] Found vcfuniq - /usr/local/bin/vcfuniq [17:27:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:27:39] Found gzip - /bin/gzip [17:27:39] Found vt - /usr/local/bin/vt [17:27:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:27:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:27:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:27:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:27:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:27:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:27:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:27:40] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:27:49] This is snippy 4.6.0
Show full stderr[17:27:49] This is snippy 4.6.0 [17:27:49] Written by Torsten Seemann [17:27:49] Obtained from https://github.com/tseemann/snippy [17:27:49] Detected operating system: linux [17:27:49] Enabling bundled linux tools. [17:27:49] Found bwa - /usr/local/bin/bwa [17:27:49] Found bcftools - /usr/local/bin/bcftools [17:27:49] Found samtools - /usr/local/bin/samtools [17:27:49] Found java - /usr/local/bin/java [17:27:49] Found snpEff - /usr/local/bin/snpEff [17:27:49] Found samclip - /usr/local/bin/samclip [17:27:49] Found seqtk - /usr/local/bin/seqtk [17:27:49] Found parallel - /usr/local/bin/parallel [17:27:49] Found freebayes - /usr/local/bin/freebayes [17:27:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:27:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:27:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:27:49] Found vcfuniq - /usr/local/bin/vcfuniq [17:27:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:27:49] Found gzip - /bin/gzip [17:27:49] Found vt - /usr/local/bin/vt [17:27:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:27:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:27:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:27:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:27:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:27:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:27:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:27:50] Please supply a reference FASTA/GBK/EMBL file with --reference
1[18:03:21] This is snippy 4.6.0
Show full stderr[18:03:21] This is snippy 4.6.0 [18:03:21] Written by Torsten Seemann [18:03:21] Obtained from https://github.com/tseemann/snippy [18:03:21] Detected operating system: linux [18:03:21] Enabling bundled linux tools. [18:03:21] Found bwa - /usr/local/bin/bwa [18:03:21] Found bcftools - /usr/local/bin/bcftools [18:03:21] Found samtools - /usr/local/bin/samtools [18:03:21] Found java - /usr/local/bin/java [18:03:21] Found snpEff - /usr/local/bin/snpEff [18:03:21] Found samclip - /usr/local/bin/samclip [18:03:21] Found seqtk - /usr/local/bin/seqtk [18:03:21] Found parallel - /usr/local/bin/parallel [18:03:21] Found freebayes - /usr/local/bin/freebayes [18:03:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [18:03:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [18:03:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [18:03:22] Found vcfuniq - /usr/local/bin/vcfuniq [18:03:22] Found vcffirstheader - /usr/local/bin/vcffirstheader [18:03:22] Found gzip - /bin/gzip [18:03:22] Found vt - /usr/local/bin/vt [18:03:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [18:03:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [18:03:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [18:03:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [18:03:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [18:03:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [18:03:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [18:03:22] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:39:00] This is snippy 4.6.0
Show full stderr[17:39:00] This is snippy 4.6.0 [17:39:00] Written by Torsten Seemann [17:39:00] Obtained from https://github.com/tseemann/snippy [17:39:00] Detected operating system: linux [17:39:00] Enabling bundled linux tools. [17:39:00] Found bwa - /usr/local/bin/bwa [17:39:00] Found bcftools - /usr/local/bin/bcftools [17:39:00] Found samtools - /usr/local/bin/samtools [17:39:00] Found java - /usr/local/bin/java [17:39:00] Found snpEff - /usr/local/bin/snpEff [17:39:00] Found samclip - /usr/local/bin/samclip [17:39:00] Found seqtk - /usr/local/bin/seqtk [17:39:00] Found parallel - /usr/local/bin/parallel [17:39:00] Found freebayes - /usr/local/bin/freebayes [17:39:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:39:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:39:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:39:00] Found vcfuniq - /usr/local/bin/vcfuniq [17:39:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:39:00] Found gzip - /bin/gzip [17:39:00] Found vt - /usr/local/bin/vt [17:39:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:39:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:39:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:39:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:39:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:39:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:39:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:39:01] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:39:33] This is snippy 4.6.0
Show full stderr[17:39:33] This is snippy 4.6.0 [17:39:33] Written by Torsten Seemann [17:39:33] Obtained from https://github.com/tseemann/snippy [17:39:33] Detected operating system: linux [17:39:33] Enabling bundled linux tools. [17:39:33] Found bwa - /usr/local/bin/bwa [17:39:33] Found bcftools - /usr/local/bin/bcftools [17:39:33] Found samtools - /usr/local/bin/samtools [17:39:33] Found java - /usr/local/bin/java [17:39:33] Found snpEff - /usr/local/bin/snpEff [17:39:33] Found samclip - /usr/local/bin/samclip [17:39:33] Found seqtk - /usr/local/bin/seqtk [17:39:33] Found parallel - /usr/local/bin/parallel [17:39:33] Found freebayes - /usr/local/bin/freebayes [17:39:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:39:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:39:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:39:33] Found vcfuniq - /usr/local/bin/vcfuniq [17:39:33] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:39:33] Found gzip - /bin/gzip [17:39:33] Found vt - /usr/local/bin/vt [17:39:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:39:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:39:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:39:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:39:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:39:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:39:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:39:34] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:40:10] This is snippy 4.6.0
Show full stderr[17:40:10] This is snippy 4.6.0 [17:40:10] Written by Torsten Seemann [17:40:10] Obtained from https://github.com/tseemann/snippy [17:40:10] Detected operating system: linux [17:40:10] Enabling bundled linux tools. [17:40:10] Found bwa - /usr/local/bin/bwa [17:40:10] Found bcftools - /usr/local/bin/bcftools [17:40:10] Found samtools - /usr/local/bin/samtools [17:40:10] Found java - /usr/local/bin/java [17:40:10] Found snpEff - /usr/local/bin/snpEff [17:40:10] Found samclip - /usr/local/bin/samclip [17:40:10] Found seqtk - /usr/local/bin/seqtk [17:40:10] Found parallel - /usr/local/bin/parallel [17:40:10] Found freebayes - /usr/local/bin/freebayes [17:40:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:40:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:40:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:40:10] Found vcfuniq - /usr/local/bin/vcfuniq [17:40:10] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:40:10] Found gzip - /bin/gzip [17:40:10] Found vt - /usr/local/bin/vt [17:40:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:40:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:40:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:40:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:40:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:40:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:40:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:40:11] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:40:16] This is snippy 4.6.0
Show full stderr[17:40:16] This is snippy 4.6.0 [17:40:16] Written by Torsten Seemann [17:40:16] Obtained from https://github.com/tseemann/snippy [17:40:16] Detected operating system: linux [17:40:16] Enabling bundled linux tools. [17:40:16] Found bwa - /usr/local/bin/bwa [17:40:16] Found bcftools - /usr/local/bin/bcftools [17:40:16] Found samtools - /usr/local/bin/samtools [17:40:16] Found java - /usr/local/bin/java [17:40:16] Found snpEff - /usr/local/bin/snpEff [17:40:17] Found samclip - /usr/local/bin/samclip [17:40:17] Found seqtk - /usr/local/bin/seqtk [17:40:17] Found parallel - /usr/local/bin/parallel [17:40:17] Found freebayes - /usr/local/bin/freebayes [17:40:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:40:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:40:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:40:17] Found vcfuniq - /usr/local/bin/vcfuniq [17:40:17] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:40:17] Found gzip - /bin/gzip [17:40:17] Found vt - /usr/local/bin/vt [17:40:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:40:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:40:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:40:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:40:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:40:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:40:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:40:18] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:40:31] This is snippy 4.6.0
Show full stderr[17:40:31] This is snippy 4.6.0 [17:40:31] Written by Torsten Seemann [17:40:31] Obtained from https://github.com/tseemann/snippy [17:40:31] Detected operating system: linux [17:40:31] Enabling bundled linux tools. [17:40:31] Found bwa - /usr/local/bin/bwa [17:40:31] Found bcftools - /usr/local/bin/bcftools [17:40:31] Found samtools - /usr/local/bin/samtools [17:40:31] Found java - /usr/local/bin/java [17:40:31] Found snpEff - /usr/local/bin/snpEff [17:40:31] Found samclip - /usr/local/bin/samclip [17:40:31] Found seqtk - /usr/local/bin/seqtk [17:40:31] Found parallel - /usr/local/bin/parallel [17:40:31] Found freebayes - /usr/local/bin/freebayes [17:40:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:40:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:40:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:40:31] Found vcfuniq - /usr/local/bin/vcfuniq [17:40:31] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:40:31] Found gzip - /bin/gzip [17:40:31] Found vt - /usr/local/bin/vt [17:40:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:40:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:40:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:40:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:40:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:40:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:40:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:40:32] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:40:54] This is snippy 4.6.0
Show full stderr[17:40:54] This is snippy 4.6.0 [17:40:54] Written by Torsten Seemann [17:40:54] Obtained from https://github.com/tseemann/snippy [17:40:54] Detected operating system: linux [17:40:54] Enabling bundled linux tools. [17:40:54] Found bwa - /usr/local/bin/bwa [17:40:54] Found bcftools - /usr/local/bin/bcftools [17:40:54] Found samtools - /usr/local/bin/samtools [17:40:54] Found java - /usr/local/bin/java [17:40:54] Found snpEff - /usr/local/bin/snpEff [17:40:54] Found samclip - /usr/local/bin/samclip [17:40:54] Found seqtk - /usr/local/bin/seqtk [17:40:54] Found parallel - /usr/local/bin/parallel [17:40:54] Found freebayes - /usr/local/bin/freebayes [17:40:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:40:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:40:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:40:54] Found vcfuniq - /usr/local/bin/vcfuniq [17:40:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:40:54] Found gzip - /bin/gzip [17:40:54] Found vt - /usr/local/bin/vt [17:40:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:40:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:40:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:40:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:40:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:40:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:40:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:40:55] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:37:44] This is snippy 4.6.0
Show full stderr[17:37:44] This is snippy 4.6.0 [17:37:44] Written by Torsten Seemann [17:37:44] Obtained from https://github.com/tseemann/snippy [17:37:44] Detected operating system: linux [17:37:44] Enabling bundled linux tools. [17:37:44] Found bwa - /usr/local/bin/bwa [17:37:44] Found bcftools - /usr/local/bin/bcftools [17:37:44] Found samtools - /usr/local/bin/samtools [17:37:44] Found java - /usr/local/bin/java [17:37:44] Found snpEff - /usr/local/bin/snpEff [17:37:44] Found samclip - /usr/local/bin/samclip [17:37:44] Found seqtk - /usr/local/bin/seqtk [17:37:44] Found parallel - /usr/local/bin/parallel [17:37:44] Found freebayes - /usr/local/bin/freebayes [17:37:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:37:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:37:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:37:45] Found vcfuniq - /usr/local/bin/vcfuniq [17:37:45] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:37:45] Found gzip - /bin/gzip [17:37:45] Found vt - /usr/local/bin/vt [17:37:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:37:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:37:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:37:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:37:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:37:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:37:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:37:46] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:38:48] This is snippy 4.6.0
Show full stderr[17:38:48] This is snippy 4.6.0 [17:38:48] Written by Torsten Seemann [17:38:48] Obtained from https://github.com/tseemann/snippy [17:38:48] Detected operating system: linux [17:38:48] Enabling bundled linux tools. [17:38:48] Found bwa - /usr/local/bin/bwa [17:38:48] Found bcftools - /usr/local/bin/bcftools [17:38:48] Found samtools - /usr/local/bin/samtools [17:38:48] Found java - /usr/local/bin/java [17:38:48] Found snpEff - /usr/local/bin/snpEff [17:38:48] Found samclip - /usr/local/bin/samclip [17:38:48] Found seqtk - /usr/local/bin/seqtk [17:38:48] Found parallel - /usr/local/bin/parallel [17:38:48] Found freebayes - /usr/local/bin/freebayes [17:38:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:38:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:38:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:38:48] Found vcfuniq - /usr/local/bin/vcfuniq [17:38:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:38:48] Found gzip - /bin/gzip [17:38:48] Found vt - /usr/local/bin/vt [17:38:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:38:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:38:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:38:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:38:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:38:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:38:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:38:49] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:39:21] This is snippy 4.6.0
Show full stderr[17:39:21] This is snippy 4.6.0 [17:39:21] Written by Torsten Seemann [17:39:21] Obtained from https://github.com/tseemann/snippy [17:39:21] Detected operating system: linux [17:39:21] Enabling bundled linux tools. [17:39:21] Found bwa - /usr/local/bin/bwa [17:39:21] Found bcftools - /usr/local/bin/bcftools [17:39:21] Found samtools - /usr/local/bin/samtools [17:39:21] Found java - /usr/local/bin/java [17:39:21] Found snpEff - /usr/local/bin/snpEff [17:39:21] Found samclip - /usr/local/bin/samclip [17:39:21] Found seqtk - /usr/local/bin/seqtk [17:39:21] Found parallel - /usr/local/bin/parallel [17:39:21] Found freebayes - /usr/local/bin/freebayes [17:39:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:39:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:39:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:39:21] Found vcfuniq - /usr/local/bin/vcfuniq [17:39:21] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:39:21] Found gzip - /bin/gzip [17:39:21] Found vt - /usr/local/bin/vt [17:39:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:39:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:39:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:39:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:39:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:39:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:39:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:39:22] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:43:07] This is snippy 4.6.0
Show full stderr[17:43:07] This is snippy 4.6.0 [17:43:07] Written by Torsten Seemann [17:43:07] Obtained from https://github.com/tseemann/snippy [17:43:07] Detected operating system: linux [17:43:07] Enabling bundled linux tools. [17:43:07] Found bwa - /usr/local/bin/bwa [17:43:07] Found bcftools - /usr/local/bin/bcftools [17:43:08] Found samtools - /usr/local/bin/samtools [17:43:08] Found java - /usr/local/bin/java [17:43:08] Found snpEff - /usr/local/bin/snpEff [17:43:08] Found samclip - /usr/local/bin/samclip [17:43:08] Found seqtk - /usr/local/bin/seqtk [17:43:08] Found parallel - /usr/local/bin/parallel [17:43:08] Found freebayes - /usr/local/bin/freebayes [17:43:08] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:43:08] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:43:08] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:43:08] Found vcfuniq - /usr/local/bin/vcfuniq [17:43:08] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:43:08] Found gzip - /bin/gzip [17:43:08] Found vt - /usr/local/bin/vt [17:43:08] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:43:08] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:43:08] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:43:08] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:43:08] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:43:09] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:43:09] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:43:09] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:43:14] This is snippy 4.6.0
Show full stderr[17:43:14] This is snippy 4.6.0 [17:43:14] Written by Torsten Seemann [17:43:14] Obtained from https://github.com/tseemann/snippy [17:43:14] Detected operating system: linux [17:43:14] Enabling bundled linux tools. [17:43:14] Found bwa - /usr/local/bin/bwa [17:43:14] Found bcftools - /usr/local/bin/bcftools [17:43:14] Found samtools - /usr/local/bin/samtools [17:43:14] Found java - /usr/local/bin/java [17:43:14] Found snpEff - /usr/local/bin/snpEff [17:43:14] Found samclip - /usr/local/bin/samclip [17:43:14] Found seqtk - /usr/local/bin/seqtk [17:43:14] Found parallel - /usr/local/bin/parallel [17:43:14] Found freebayes - /usr/local/bin/freebayes [17:43:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:43:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:43:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:43:14] Found vcfuniq - /usr/local/bin/vcfuniq [17:43:14] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:43:14] Found gzip - /bin/gzip [17:43:14] Found vt - /usr/local/bin/vt [17:43:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:43:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:43:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:43:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:43:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:43:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:43:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:43:15] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:43:43] This is snippy 4.6.0
Show full stderr[17:43:43] This is snippy 4.6.0 [17:43:43] Written by Torsten Seemann [17:43:43] Obtained from https://github.com/tseemann/snippy [17:43:43] Detected operating system: linux [17:43:43] Enabling bundled linux tools. [17:43:43] Found bwa - /usr/local/bin/bwa [17:43:44] Found bcftools - /usr/local/bin/bcftools [17:43:44] Found samtools - /usr/local/bin/samtools [17:43:44] Found java - /usr/local/bin/java [17:43:44] Found snpEff - /usr/local/bin/snpEff [17:43:44] Found samclip - /usr/local/bin/samclip [17:43:44] Found seqtk - /usr/local/bin/seqtk [17:43:44] Found parallel - /usr/local/bin/parallel [17:43:44] Found freebayes - /usr/local/bin/freebayes [17:43:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:43:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:43:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:43:44] Found vcfuniq - /usr/local/bin/vcfuniq [17:43:44] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:43:44] Found gzip - /bin/gzip [17:43:44] Found vt - /usr/local/bin/vt [17:43:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:43:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:43:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:43:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:43:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:43:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:43:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:43:45] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:44:32] This is snippy 4.6.0
Show full stderr[17:44:32] This is snippy 4.6.0 [17:44:32] Written by Torsten Seemann [17:44:32] Obtained from https://github.com/tseemann/snippy [17:44:32] Detected operating system: linux [17:44:32] Enabling bundled linux tools. [17:44:32] Found bwa - /usr/local/bin/bwa [17:44:32] Found bcftools - /usr/local/bin/bcftools [17:44:33] Found samtools - /usr/local/bin/samtools [17:44:33] Found java - /usr/local/bin/java [17:44:33] Found snpEff - /usr/local/bin/snpEff [17:44:33] Found samclip - /usr/local/bin/samclip [17:44:33] Found seqtk - /usr/local/bin/seqtk [17:44:33] Found parallel - /usr/local/bin/parallel [17:44:33] Found freebayes - /usr/local/bin/freebayes [17:44:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:44:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:44:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:44:33] Found vcfuniq - /usr/local/bin/vcfuniq [17:44:33] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:44:33] Found gzip - /bin/gzip [17:44:33] Found vt - /usr/local/bin/vt [17:44:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:44:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:44:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:44:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:44:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:44:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:44:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:44:34] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:44:42] This is snippy 4.6.0
Show full stderr[17:44:42] This is snippy 4.6.0 [17:44:42] Written by Torsten Seemann [17:44:42] Obtained from https://github.com/tseemann/snippy [17:44:42] Detected operating system: linux [17:44:42] Enabling bundled linux tools. [17:44:42] Found bwa - /usr/local/bin/bwa [17:44:42] Found bcftools - /usr/local/bin/bcftools [17:44:42] Found samtools - /usr/local/bin/samtools [17:44:42] Found java - /usr/local/bin/java [17:44:42] Found snpEff - /usr/local/bin/snpEff [17:44:42] Found samclip - /usr/local/bin/samclip [17:44:42] Found seqtk - /usr/local/bin/seqtk [17:44:42] Found parallel - /usr/local/bin/parallel [17:44:42] Found freebayes - /usr/local/bin/freebayes [17:44:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:44:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:44:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:44:42] Found vcfuniq - /usr/local/bin/vcfuniq [17:44:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:44:42] Found gzip - /bin/gzip [17:44:42] Found vt - /usr/local/bin/vt [17:44:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:44:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:44:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:44:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:44:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:44:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:44:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:44:43] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:45:09] This is snippy 4.6.0
Show full stderr[17:45:09] This is snippy 4.6.0 [17:45:09] Written by Torsten Seemann [17:45:09] Obtained from https://github.com/tseemann/snippy [17:45:09] Detected operating system: linux [17:45:09] Enabling bundled linux tools. [17:45:09] Found bwa - /usr/local/bin/bwa [17:45:09] Found bcftools - /usr/local/bin/bcftools [17:45:09] Found samtools - /usr/local/bin/samtools [17:45:09] Found java - /usr/local/bin/java [17:45:09] Found snpEff - /usr/local/bin/snpEff [17:45:09] Found samclip - /usr/local/bin/samclip [17:45:09] Found seqtk - /usr/local/bin/seqtk [17:45:09] Found parallel - /usr/local/bin/parallel [17:45:09] Found freebayes - /usr/local/bin/freebayes [17:45:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:45:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:45:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:45:09] Found vcfuniq - /usr/local/bin/vcfuniq [17:45:09] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:45:09] Found gzip - /bin/gzip [17:45:09] Found vt - /usr/local/bin/vt [17:45:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:45:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:45:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:45:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:45:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:45:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:45:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:45:10] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:45:12] This is snippy 4.6.0
Show full stderr[17:45:12] This is snippy 4.6.0 [17:45:12] Written by Torsten Seemann [17:45:12] Obtained from https://github.com/tseemann/snippy [17:45:12] Detected operating system: linux [17:45:12] Enabling bundled linux tools. [17:45:12] Found bwa - /usr/local/bin/bwa [17:45:12] Found bcftools - /usr/local/bin/bcftools [17:45:12] Found samtools - /usr/local/bin/samtools [17:45:13] Found java - /usr/local/bin/java [17:45:13] Found snpEff - /usr/local/bin/snpEff [17:45:13] Found samclip - /usr/local/bin/samclip [17:45:13] Found seqtk - /usr/local/bin/seqtk [17:45:13] Found parallel - /usr/local/bin/parallel [17:45:13] Found freebayes - /usr/local/bin/freebayes [17:45:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:45:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:45:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:45:13] Found vcfuniq - /usr/local/bin/vcfuniq [17:45:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:45:13] Found gzip - /bin/gzip [17:45:13] Found vt - /usr/local/bin/vt [17:45:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:45:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:45:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:45:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:45:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:45:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:45:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:45:13] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:37:51] This is snippy 4.6.0
Show full stderr[17:37:51] This is snippy 4.6.0 [17:37:51] Written by Torsten Seemann [17:37:51] Obtained from https://github.com/tseemann/snippy [17:37:51] Detected operating system: linux [17:37:51] Enabling bundled linux tools. [17:37:51] Found bwa - /usr/local/bin/bwa [17:37:51] Found bcftools - /usr/local/bin/bcftools [17:37:51] Found samtools - /usr/local/bin/samtools [17:37:51] Found java - /usr/local/bin/java [17:37:51] Found snpEff - /usr/local/bin/snpEff [17:37:51] Found samclip - /usr/local/bin/samclip [17:37:51] Found seqtk - /usr/local/bin/seqtk [17:37:51] Found parallel - /usr/local/bin/parallel [17:37:51] Found freebayes - /usr/local/bin/freebayes [17:37:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:37:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:37:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:37:51] Found vcfuniq - /usr/local/bin/vcfuniq [17:37:51] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:37:51] Found gzip - /bin/gzip [17:37:51] Found vt - /usr/local/bin/vt [17:37:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:37:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:37:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:37:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:37:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:37:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:37:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:37:52] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:39:03] This is snippy 4.6.0
Show full stderr[17:39:03] This is snippy 4.6.0 [17:39:03] Written by Torsten Seemann [17:39:03] Obtained from https://github.com/tseemann/snippy [17:39:03] Detected operating system: linux [17:39:03] Enabling bundled linux tools. [17:39:03] Found bwa - /usr/local/bin/bwa [17:39:03] Found bcftools - /usr/local/bin/bcftools [17:39:03] Found samtools - /usr/local/bin/samtools [17:39:03] Found java - /usr/local/bin/java [17:39:03] Found snpEff - /usr/local/bin/snpEff [17:39:03] Found samclip - /usr/local/bin/samclip [17:39:03] Found seqtk - /usr/local/bin/seqtk [17:39:03] Found parallel - /usr/local/bin/parallel [17:39:03] Found freebayes - /usr/local/bin/freebayes [17:39:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:39:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:39:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:39:03] Found vcfuniq - /usr/local/bin/vcfuniq [17:39:03] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:39:03] Found gzip - /bin/gzip [17:39:03] Found vt - /usr/local/bin/vt [17:39:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:39:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:39:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:39:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:39:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:39:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:39:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:39:04] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:39:45] This is snippy 4.6.0
Show full stderr[17:39:45] This is snippy 4.6.0 [17:39:45] Written by Torsten Seemann [17:39:45] Obtained from https://github.com/tseemann/snippy [17:39:45] Detected operating system: linux [17:39:45] Enabling bundled linux tools. [17:39:45] Found bwa - /usr/local/bin/bwa [17:39:45] Found bcftools - /usr/local/bin/bcftools [17:39:45] Found samtools - /usr/local/bin/samtools [17:39:45] Found java - /usr/local/bin/java [17:39:45] Found snpEff - /usr/local/bin/snpEff [17:39:45] Found samclip - /usr/local/bin/samclip [17:39:45] Found seqtk - /usr/local/bin/seqtk [17:39:45] Found parallel - /usr/local/bin/parallel [17:39:45] Found freebayes - /usr/local/bin/freebayes [17:39:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:39:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:39:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:39:45] Found vcfuniq - /usr/local/bin/vcfuniq [17:39:45] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:39:45] Found gzip - /bin/gzip [17:39:45] Found vt - /usr/local/bin/vt [17:39:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:39:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:39:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:39:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:39:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:39:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:39:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:39:46] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:40:04] This is snippy 4.6.0
Show full stderr[17:40:04] This is snippy 4.6.0 [17:40:04] Written by Torsten Seemann [17:40:04] Obtained from https://github.com/tseemann/snippy [17:40:04] Detected operating system: linux [17:40:04] Enabling bundled linux tools. [17:40:04] Found bwa - /usr/local/bin/bwa [17:40:04] Found bcftools - /usr/local/bin/bcftools [17:40:04] Found samtools - /usr/local/bin/samtools [17:40:04] Found java - /usr/local/bin/java [17:40:04] Found snpEff - /usr/local/bin/snpEff [17:40:04] Found samclip - /usr/local/bin/samclip [17:40:04] Found seqtk - /usr/local/bin/seqtk [17:40:04] Found parallel - /usr/local/bin/parallel [17:40:04] Found freebayes - /usr/local/bin/freebayes [17:40:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:40:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:40:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:40:04] Found vcfuniq - /usr/local/bin/vcfuniq [17:40:04] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:40:04] Found gzip - /bin/gzip [17:40:04] Found vt - /usr/local/bin/vt [17:40:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:40:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:40:05] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:40:05] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:40:05] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:40:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:40:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:40:05] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:40:12] This is snippy 4.6.0
Show full stderr[17:40:12] This is snippy 4.6.0 [17:40:12] Written by Torsten Seemann [17:40:12] Obtained from https://github.com/tseemann/snippy [17:40:12] Detected operating system: linux [17:40:12] Enabling bundled linux tools. [17:40:12] Found bwa - /usr/local/bin/bwa [17:40:12] Found bcftools - /usr/local/bin/bcftools [17:40:12] Found samtools - /usr/local/bin/samtools [17:40:12] Found java - /usr/local/bin/java [17:40:12] Found snpEff - /usr/local/bin/snpEff [17:40:12] Found samclip - /usr/local/bin/samclip [17:40:12] Found seqtk - /usr/local/bin/seqtk [17:40:12] Found parallel - /usr/local/bin/parallel [17:40:12] Found freebayes - /usr/local/bin/freebayes [17:40:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:40:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:40:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:40:12] Found vcfuniq - /usr/local/bin/vcfuniq [17:40:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:40:12] Found gzip - /bin/gzip [17:40:12] Found vt - /usr/local/bin/vt [17:40:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:40:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:40:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:40:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:40:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:40:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:40:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:40:13] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:41:15] This is snippy 4.6.0
Show full stderr[17:41:15] This is snippy 4.6.0 [17:41:15] Written by Torsten Seemann [17:41:15] Obtained from https://github.com/tseemann/snippy [17:41:15] Detected operating system: linux [17:41:15] Enabling bundled linux tools. [17:41:15] Found bwa - /usr/local/bin/bwa [17:41:15] Found bcftools - /usr/local/bin/bcftools [17:41:15] Found samtools - /usr/local/bin/samtools [17:41:15] Found java - /usr/local/bin/java [17:41:15] Found snpEff - /usr/local/bin/snpEff [17:41:15] Found samclip - /usr/local/bin/samclip [17:41:15] Found seqtk - /usr/local/bin/seqtk [17:41:15] Found parallel - /usr/local/bin/parallel [17:41:15] Found freebayes - /usr/local/bin/freebayes [17:41:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:41:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:41:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:41:16] Found vcfuniq - /usr/local/bin/vcfuniq [17:41:16] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:41:16] Found gzip - /bin/gzip [17:41:16] Found vt - /usr/local/bin/vt [17:41:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:41:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:41:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:41:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:41:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:41:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:41:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:41:17] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:41:48] This is snippy 4.6.0
Show full stderr[17:41:48] This is snippy 4.6.0 [17:41:48] Written by Torsten Seemann [17:41:48] Obtained from https://github.com/tseemann/snippy [17:41:48] Detected operating system: linux [17:41:48] Enabling bundled linux tools. [17:41:48] Found bwa - /usr/local/bin/bwa [17:41:48] Found bcftools - /usr/local/bin/bcftools [17:41:48] Found samtools - /usr/local/bin/samtools [17:41:48] Found java - /usr/local/bin/java [17:41:48] Found snpEff - /usr/local/bin/snpEff [17:41:48] Found samclip - /usr/local/bin/samclip [17:41:48] Found seqtk - /usr/local/bin/seqtk [17:41:48] Found parallel - /usr/local/bin/parallel [17:41:48] Found freebayes - /usr/local/bin/freebayes [17:41:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:41:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:41:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:41:48] Found vcfuniq - /usr/local/bin/vcfuniq [17:41:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:41:48] Found gzip - /bin/gzip [17:41:48] Found vt - /usr/local/bin/vt [17:41:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:41:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:41:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:41:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:41:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:41:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:41:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:41:49] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:41:53] This is snippy 4.6.0
Show full stderr[17:41:53] This is snippy 4.6.0 [17:41:53] Written by Torsten Seemann [17:41:53] Obtained from https://github.com/tseemann/snippy [17:41:53] Detected operating system: linux [17:41:53] Enabling bundled linux tools. [17:41:53] Found bwa - /usr/local/bin/bwa [17:41:53] Found bcftools - /usr/local/bin/bcftools [17:41:53] Found samtools - /usr/local/bin/samtools [17:41:53] Found java - /usr/local/bin/java [17:41:53] Found snpEff - /usr/local/bin/snpEff [17:41:53] Found samclip - /usr/local/bin/samclip [17:41:53] Found seqtk - /usr/local/bin/seqtk [17:41:53] Found parallel - /usr/local/bin/parallel [17:41:53] Found freebayes - /usr/local/bin/freebayes [17:41:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:41:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:41:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:41:53] Found vcfuniq - /usr/local/bin/vcfuniq [17:41:53] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:41:53] Found gzip - /bin/gzip [17:41:53] Found vt - /usr/local/bin/vt [17:41:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:41:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:41:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:41:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:41:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:41:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:41:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:41:54] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:42:19] This is snippy 4.6.0
Show full stderr[17:42:19] This is snippy 4.6.0 [17:42:19] Written by Torsten Seemann [17:42:19] Obtained from https://github.com/tseemann/snippy [17:42:19] Detected operating system: linux [17:42:19] Enabling bundled linux tools. [17:42:19] Found bwa - /usr/local/bin/bwa [17:42:19] Found bcftools - /usr/local/bin/bcftools [17:42:19] Found samtools - /usr/local/bin/samtools [17:42:19] Found java - /usr/local/bin/java [17:42:19] Found snpEff - /usr/local/bin/snpEff [17:42:19] Found samclip - /usr/local/bin/samclip [17:42:19] Found seqtk - /usr/local/bin/seqtk [17:42:19] Found parallel - /usr/local/bin/parallel [17:42:19] Found freebayes - /usr/local/bin/freebayes [17:42:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:42:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:42:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:42:19] Found vcfuniq - /usr/local/bin/vcfuniq [17:42:19] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:42:19] Found gzip - /bin/gzip [17:42:19] Found vt - /usr/local/bin/vt [17:42:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:42:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:42:20] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:42:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:42:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:42:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:42:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:42:20] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:38:01] This is snippy 4.6.0
Show full stderr[17:38:01] This is snippy 4.6.0 [17:38:01] Written by Torsten Seemann [17:38:01] Obtained from https://github.com/tseemann/snippy [17:38:01] Detected operating system: linux [17:38:01] Enabling bundled linux tools. [17:38:01] Found bwa - /usr/local/bin/bwa [17:38:01] Found bcftools - /usr/local/bin/bcftools [17:38:01] Found samtools - /usr/local/bin/samtools [17:38:01] Found java - /usr/local/bin/java [17:38:01] Found snpEff - /usr/local/bin/snpEff [17:38:01] Found samclip - /usr/local/bin/samclip [17:38:01] Found seqtk - /usr/local/bin/seqtk [17:38:01] Found parallel - /usr/local/bin/parallel [17:38:01] Found freebayes - /usr/local/bin/freebayes [17:38:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:38:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:38:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:38:01] Found vcfuniq - /usr/local/bin/vcfuniq [17:38:01] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:38:01] Found gzip - /bin/gzip [17:38:01] Found vt - /usr/local/bin/vt [17:38:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:38:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:38:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:38:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:38:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:38:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:38:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:38:02] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:39:30] This is snippy 4.6.0
Show full stderr[17:39:30] This is snippy 4.6.0 [17:39:30] Written by Torsten Seemann [17:39:30] Obtained from https://github.com/tseemann/snippy [17:39:30] Detected operating system: linux [17:39:30] Enabling bundled linux tools. [17:39:30] Found bwa - /usr/local/bin/bwa [17:39:30] Found bcftools - /usr/local/bin/bcftools [17:39:30] Found samtools - /usr/local/bin/samtools [17:39:31] Found java - /usr/local/bin/java [17:39:31] Found snpEff - /usr/local/bin/snpEff [17:39:31] Found samclip - /usr/local/bin/samclip [17:39:31] Found seqtk - /usr/local/bin/seqtk [17:39:31] Found parallel - /usr/local/bin/parallel [17:39:31] Found freebayes - /usr/local/bin/freebayes [17:39:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:39:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:39:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:39:31] Found vcfuniq - /usr/local/bin/vcfuniq [17:39:31] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:39:31] Found gzip - /bin/gzip [17:39:31] Found vt - /usr/local/bin/vt [17:39:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:39:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:39:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:39:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:39:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:39:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:39:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:39:32] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:39:24] This is snippy 4.6.0
Show full stderr[17:39:24] This is snippy 4.6.0 [17:39:24] Written by Torsten Seemann [17:39:24] Obtained from https://github.com/tseemann/snippy [17:39:24] Detected operating system: linux [17:39:24] Enabling bundled linux tools. [17:39:24] Found bwa - /usr/local/bin/bwa [17:39:24] Found bcftools - /usr/local/bin/bcftools [17:39:24] Found samtools - /usr/local/bin/samtools [17:39:24] Found java - /usr/local/bin/java [17:39:24] Found snpEff - /usr/local/bin/snpEff [17:39:24] Found samclip - /usr/local/bin/samclip [17:39:24] Found seqtk - /usr/local/bin/seqtk [17:39:24] Found parallel - /usr/local/bin/parallel [17:39:24] Found freebayes - /usr/local/bin/freebayes [17:39:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:39:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:39:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:39:24] Found vcfuniq - /usr/local/bin/vcfuniq [17:39:24] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:39:24] Found gzip - /bin/gzip [17:39:24] Found vt - /usr/local/bin/vt [17:39:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:39:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:39:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:39:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:39:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:39:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:39:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:39:25] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:39:39] This is snippy 4.6.0
Show full stderr[17:39:39] This is snippy 4.6.0 [17:39:39] Written by Torsten Seemann [17:39:39] Obtained from https://github.com/tseemann/snippy [17:39:39] Detected operating system: linux [17:39:39] Enabling bundled linux tools. [17:39:39] Found bwa - /usr/local/bin/bwa [17:39:39] Found bcftools - /usr/local/bin/bcftools [17:39:39] Found samtools - /usr/local/bin/samtools [17:39:39] Found java - /usr/local/bin/java [17:39:39] Found snpEff - /usr/local/bin/snpEff [17:39:39] Found samclip - /usr/local/bin/samclip [17:39:39] Found seqtk - /usr/local/bin/seqtk [17:39:39] Found parallel - /usr/local/bin/parallel [17:39:39] Found freebayes - /usr/local/bin/freebayes [17:39:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:39:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:39:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:39:39] Found vcfuniq - /usr/local/bin/vcfuniq [17:39:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:39:39] Found gzip - /bin/gzip [17:39:39] Found vt - /usr/local/bin/vt [17:39:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:39:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:39:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:39:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:39:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:39:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:39:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:39:40] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:40:00] This is snippy 4.6.0
Show full stderr[17:40:00] This is snippy 4.6.0 [17:40:00] Written by Torsten Seemann [17:40:00] Obtained from https://github.com/tseemann/snippy [17:40:00] Detected operating system: linux [17:40:00] Enabling bundled linux tools. [17:40:00] Found bwa - /usr/local/bin/bwa [17:40:00] Found bcftools - /usr/local/bin/bcftools [17:40:00] Found samtools - /usr/local/bin/samtools [17:40:00] Found java - /usr/local/bin/java [17:40:00] Found snpEff - /usr/local/bin/snpEff [17:40:00] Found samclip - /usr/local/bin/samclip [17:40:00] Found seqtk - /usr/local/bin/seqtk [17:40:00] Found parallel - /usr/local/bin/parallel [17:40:00] Found freebayes - /usr/local/bin/freebayes [17:40:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:40:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:40:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:40:00] Found vcfuniq - /usr/local/bin/vcfuniq [17:40:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:40:00] Found gzip - /bin/gzip [17:40:00] Found vt - /usr/local/bin/vt [17:40:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:40:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:40:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:40:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:40:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:40:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:40:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:40:01] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:40:25] This is snippy 4.6.0
Show full stderr[17:40:25] This is snippy 4.6.0 [17:40:25] Written by Torsten Seemann [17:40:25] Obtained from https://github.com/tseemann/snippy [17:40:25] Detected operating system: linux [17:40:25] Enabling bundled linux tools. [17:40:25] Found bwa - /usr/local/bin/bwa [17:40:25] Found bcftools - /usr/local/bin/bcftools [17:40:26] Found samtools - /usr/local/bin/samtools [17:40:26] Found java - /usr/local/bin/java [17:40:26] Found snpEff - /usr/local/bin/snpEff [17:40:26] Found samclip - /usr/local/bin/samclip [17:40:26] Found seqtk - /usr/local/bin/seqtk [17:40:26] Found parallel - /usr/local/bin/parallel [17:40:26] Found freebayes - /usr/local/bin/freebayes [17:40:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:40:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:40:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:40:26] Found vcfuniq - /usr/local/bin/vcfuniq [17:40:26] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:40:26] Found gzip - /bin/gzip [17:40:26] Found vt - /usr/local/bin/vt [17:40:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:40:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:40:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:40:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:40:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:40:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:40:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:40:27] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:40:34] This is snippy 4.6.0
Show full stderr[17:40:34] This is snippy 4.6.0 [17:40:34] Written by Torsten Seemann [17:40:34] Obtained from https://github.com/tseemann/snippy [17:40:34] Detected operating system: linux [17:40:34] Enabling bundled linux tools. [17:40:34] Found bwa - /usr/local/bin/bwa [17:40:34] Found bcftools - /usr/local/bin/bcftools [17:40:34] Found samtools - /usr/local/bin/samtools [17:40:34] Found java - /usr/local/bin/java [17:40:34] Found snpEff - /usr/local/bin/snpEff [17:40:34] Found samclip - /usr/local/bin/samclip [17:40:34] Found seqtk - /usr/local/bin/seqtk [17:40:34] Found parallel - /usr/local/bin/parallel [17:40:34] Found freebayes - /usr/local/bin/freebayes [17:40:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:40:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:40:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:40:35] Found vcfuniq - /usr/local/bin/vcfuniq [17:40:35] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:40:35] Found gzip - /bin/gzip [17:40:35] Found vt - /usr/local/bin/vt [17:40:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:40:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:40:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:40:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:40:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:40:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:40:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:40:36] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:40:39] This is snippy 4.6.0
Show full stderr[17:40:39] This is snippy 4.6.0 [17:40:39] Written by Torsten Seemann [17:40:39] Obtained from https://github.com/tseemann/snippy [17:40:39] Detected operating system: linux [17:40:39] Enabling bundled linux tools. [17:40:39] Found bwa - /usr/local/bin/bwa [17:40:39] Found bcftools - /usr/local/bin/bcftools [17:40:39] Found samtools - /usr/local/bin/samtools [17:40:39] Found java - /usr/local/bin/java [17:40:39] Found snpEff - /usr/local/bin/snpEff [17:40:39] Found samclip - /usr/local/bin/samclip [17:40:39] Found seqtk - /usr/local/bin/seqtk [17:40:39] Found parallel - /usr/local/bin/parallel [17:40:39] Found freebayes - /usr/local/bin/freebayes [17:40:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:40:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:40:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:40:39] Found vcfuniq - /usr/local/bin/vcfuniq [17:40:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:40:39] Found gzip - /bin/gzip [17:40:39] Found vt - /usr/local/bin/vt [17:40:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:40:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:40:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:40:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:40:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:40:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:40:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:40:40] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:41:45] This is snippy 4.6.0
Show full stderr[17:41:45] This is snippy 4.6.0 [17:41:45] Written by Torsten Seemann [17:41:45] Obtained from https://github.com/tseemann/snippy [17:41:45] Detected operating system: linux [17:41:45] Enabling bundled linux tools. [17:41:45] Found bwa - /usr/local/bin/bwa [17:41:45] Found bcftools - /usr/local/bin/bcftools [17:41:45] Found samtools - /usr/local/bin/samtools [17:41:45] Found java - /usr/local/bin/java [17:41:45] Found snpEff - /usr/local/bin/snpEff [17:41:45] Found samclip - /usr/local/bin/samclip [17:41:45] Found seqtk - /usr/local/bin/seqtk [17:41:45] Found parallel - /usr/local/bin/parallel [17:41:45] Found freebayes - /usr/local/bin/freebayes [17:41:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:41:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:41:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:41:45] Found vcfuniq - /usr/local/bin/vcfuniq [17:41:45] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:41:45] Found gzip - /bin/gzip [17:41:45] Found vt - /usr/local/bin/vt [17:41:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:41:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:41:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:41:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:41:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:41:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:41:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:41:46] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:41:55] This is snippy 4.6.0
Show full stderr[17:41:55] This is snippy 4.6.0 [17:41:55] Written by Torsten Seemann [17:41:55] Obtained from https://github.com/tseemann/snippy [17:41:55] Detected operating system: linux [17:41:55] Enabling bundled linux tools. [17:41:55] Found bwa - /usr/local/bin/bwa [17:41:55] Found bcftools - /usr/local/bin/bcftools [17:41:55] Found samtools - /usr/local/bin/samtools [17:41:55] Found java - /usr/local/bin/java [17:41:55] Found snpEff - /usr/local/bin/snpEff [17:41:55] Found samclip - /usr/local/bin/samclip [17:41:55] Found seqtk - /usr/local/bin/seqtk [17:41:55] Found parallel - /usr/local/bin/parallel [17:41:55] Found freebayes - /usr/local/bin/freebayes [17:41:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:41:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:41:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:41:55] Found vcfuniq - /usr/local/bin/vcfuniq [17:41:56] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:41:56] Found gzip - /bin/gzip [17:41:56] Found vt - /usr/local/bin/vt [17:41:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:41:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:41:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:41:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:41:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:41:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:41:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:41:57] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:41:57] This is snippy 4.6.0
Show full stderr[17:41:57] This is snippy 4.6.0 [17:41:57] Written by Torsten Seemann [17:41:57] Obtained from https://github.com/tseemann/snippy [17:41:57] Detected operating system: linux [17:41:57] Enabling bundled linux tools. [17:41:57] Found bwa - /usr/local/bin/bwa [17:41:57] Found bcftools - /usr/local/bin/bcftools [17:41:57] Found samtools - /usr/local/bin/samtools [17:41:57] Found java - /usr/local/bin/java [17:41:57] Found snpEff - /usr/local/bin/snpEff [17:41:57] Found samclip - /usr/local/bin/samclip [17:41:57] Found seqtk - /usr/local/bin/seqtk [17:41:57] Found parallel - /usr/local/bin/parallel [17:41:57] Found freebayes - /usr/local/bin/freebayes [17:41:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:41:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:41:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:41:57] Found vcfuniq - /usr/local/bin/vcfuniq [17:41:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:41:57] Found gzip - /bin/gzip [17:41:57] Found vt - /usr/local/bin/vt [17:41:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:41:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:41:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:41:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:41:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:41:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:41:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:41:58] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:42:04] This is snippy 4.6.0
Show full stderr[17:42:04] This is snippy 4.6.0 [17:42:04] Written by Torsten Seemann [17:42:04] Obtained from https://github.com/tseemann/snippy [17:42:04] Detected operating system: linux [17:42:04] Enabling bundled linux tools. [17:42:04] Found bwa - /usr/local/bin/bwa [17:42:05] Found bcftools - /usr/local/bin/bcftools [17:42:05] Found samtools - /usr/local/bin/samtools [17:42:05] Found java - /usr/local/bin/java [17:42:05] Found snpEff - /usr/local/bin/snpEff [17:42:05] Found samclip - /usr/local/bin/samclip [17:42:05] Found seqtk - /usr/local/bin/seqtk [17:42:05] Found parallel - /usr/local/bin/parallel [17:42:05] Found freebayes - /usr/local/bin/freebayes [17:42:05] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:42:05] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:42:05] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:42:05] Found vcfuniq - /usr/local/bin/vcfuniq [17:42:05] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:42:05] Found gzip - /bin/gzip [17:42:05] Found vt - /usr/local/bin/vt [17:42:05] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:42:05] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:42:05] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:42:05] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:42:05] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:42:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:42:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:42:06] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:42:16] This is snippy 4.6.0
Show full stderr[17:42:16] This is snippy 4.6.0 [17:42:16] Written by Torsten Seemann [17:42:16] Obtained from https://github.com/tseemann/snippy [17:42:16] Detected operating system: linux [17:42:16] Enabling bundled linux tools. [17:42:16] Found bwa - /usr/local/bin/bwa [17:42:16] Found bcftools - /usr/local/bin/bcftools [17:42:16] Found samtools - /usr/local/bin/samtools [17:42:16] Found java - /usr/local/bin/java [17:42:16] Found snpEff - /usr/local/bin/snpEff [17:42:16] Found samclip - /usr/local/bin/samclip [17:42:16] Found seqtk - /usr/local/bin/seqtk [17:42:16] Found parallel - /usr/local/bin/parallel [17:42:16] Found freebayes - /usr/local/bin/freebayes [17:42:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:42:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:42:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:42:16] Found vcfuniq - /usr/local/bin/vcfuniq [17:42:16] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:42:16] Found gzip - /bin/gzip [17:42:16] Found vt - /usr/local/bin/vt [17:42:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:42:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:42:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:42:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:42:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:42:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:42:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:42:17] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:42:29] This is snippy 4.6.0
Show full stderr[17:42:29] This is snippy 4.6.0 [17:42:29] Written by Torsten Seemann [17:42:29] Obtained from https://github.com/tseemann/snippy [17:42:29] Detected operating system: linux [17:42:29] Enabling bundled linux tools. [17:42:29] Found bwa - /usr/local/bin/bwa [17:42:29] Found bcftools - /usr/local/bin/bcftools [17:42:29] Found samtools - /usr/local/bin/samtools [17:42:29] Found java - /usr/local/bin/java [17:42:29] Found snpEff - /usr/local/bin/snpEff [17:42:29] Found samclip - /usr/local/bin/samclip [17:42:29] Found seqtk - /usr/local/bin/seqtk [17:42:29] Found parallel - /usr/local/bin/parallel [17:42:29] Found freebayes - /usr/local/bin/freebayes [17:42:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:42:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:42:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:42:29] Found vcfuniq - /usr/local/bin/vcfuniq [17:42:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:42:30] Found gzip - /bin/gzip [17:42:30] Found vt - /usr/local/bin/vt [17:42:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:42:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:42:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:42:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:42:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:42:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:42:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:42:31] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:43:02] This is snippy 4.6.0
Show full stderr[17:43:02] This is snippy 4.6.0 [17:43:02] Written by Torsten Seemann [17:43:02] Obtained from https://github.com/tseemann/snippy [17:43:02] Detected operating system: linux [17:43:02] Enabling bundled linux tools. [17:43:02] Found bwa - /usr/local/bin/bwa [17:43:02] Found bcftools - /usr/local/bin/bcftools [17:43:02] Found samtools - /usr/local/bin/samtools [17:43:02] Found java - /usr/local/bin/java [17:43:02] Found snpEff - /usr/local/bin/snpEff [17:43:02] Found samclip - /usr/local/bin/samclip [17:43:02] Found seqtk - /usr/local/bin/seqtk [17:43:02] Found parallel - /usr/local/bin/parallel [17:43:02] Found freebayes - /usr/local/bin/freebayes [17:43:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:43:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:43:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:43:02] Found vcfuniq - /usr/local/bin/vcfuniq [17:43:03] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:43:03] Found gzip - /bin/gzip [17:43:03] Found vt - /usr/local/bin/vt [17:43:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:43:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:43:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:43:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:43:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:43:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:43:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:43:04] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:44:14] This is snippy 4.6.0
Show full stderr[17:44:14] This is snippy 4.6.0 [17:44:14] Written by Torsten Seemann [17:44:14] Obtained from https://github.com/tseemann/snippy [17:44:14] Detected operating system: linux [17:44:14] Enabling bundled linux tools. [17:44:15] Found bwa - /usr/local/bin/bwa [17:44:15] Found bcftools - /usr/local/bin/bcftools [17:44:15] Found samtools - /usr/local/bin/samtools [17:44:15] Found java - /usr/local/bin/java [17:44:15] Found snpEff - /usr/local/bin/snpEff [17:44:15] Found samclip - /usr/local/bin/samclip [17:44:15] Found seqtk - /usr/local/bin/seqtk [17:44:15] Found parallel - /usr/local/bin/parallel [17:44:15] Found freebayes - /usr/local/bin/freebayes [17:44:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:44:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:44:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:44:15] Found vcfuniq - /usr/local/bin/vcfuniq [17:44:15] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:44:15] Found gzip - /bin/gzip [17:44:15] Found vt - /usr/local/bin/vt [17:44:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:44:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:44:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:44:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:44:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:44:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:44:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:44:16] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:44:15] This is snippy 4.6.0
Show full stderr[17:44:15] This is snippy 4.6.0 [17:44:15] Written by Torsten Seemann [17:44:15] Obtained from https://github.com/tseemann/snippy [17:44:15] Detected operating system: linux [17:44:15] Enabling bundled linux tools. [17:44:15] Found bwa - /usr/local/bin/bwa [17:44:15] Found bcftools - /usr/local/bin/bcftools [17:44:15] Found samtools - /usr/local/bin/samtools [17:44:16] Found java - /usr/local/bin/java [17:44:16] Found snpEff - /usr/local/bin/snpEff [17:44:16] Found samclip - /usr/local/bin/samclip [17:44:16] Found seqtk - /usr/local/bin/seqtk [17:44:16] Found parallel - /usr/local/bin/parallel [17:44:16] Found freebayes - /usr/local/bin/freebayes [17:44:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:44:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:44:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:44:16] Found vcfuniq - /usr/local/bin/vcfuniq [17:44:16] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:44:16] Found gzip - /bin/gzip [17:44:16] Found vt - /usr/local/bin/vt [17:44:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:44:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:44:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:44:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:44:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:44:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:44:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:44:17] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:44:45] This is snippy 4.6.0
Show full stderr[17:44:45] This is snippy 4.6.0 [17:44:45] Written by Torsten Seemann [17:44:45] Obtained from https://github.com/tseemann/snippy [17:44:45] Detected operating system: linux [17:44:45] Enabling bundled linux tools. [17:44:45] Found bwa - /usr/local/bin/bwa [17:44:45] Found bcftools - /usr/local/bin/bcftools [17:44:45] Found samtools - /usr/local/bin/samtools [17:44:45] Found java - /usr/local/bin/java [17:44:45] Found snpEff - /usr/local/bin/snpEff [17:44:45] Found samclip - /usr/local/bin/samclip [17:44:45] Found seqtk - /usr/local/bin/seqtk [17:44:45] Found parallel - /usr/local/bin/parallel [17:44:45] Found freebayes - /usr/local/bin/freebayes [17:44:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:44:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:44:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:44:45] Found vcfuniq - /usr/local/bin/vcfuniq [17:44:45] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:44:45] Found gzip - /bin/gzip [17:44:45] Found vt - /usr/local/bin/vt [17:44:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:44:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:44:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:44:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:44:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:44:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:44:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:44:46] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:44:55] This is snippy 4.6.0
Show full stderr[17:44:55] This is snippy 4.6.0 [17:44:55] Written by Torsten Seemann [17:44:55] Obtained from https://github.com/tseemann/snippy [17:44:55] Detected operating system: linux [17:44:55] Enabling bundled linux tools. [17:44:55] Found bwa - /usr/local/bin/bwa [17:44:55] Found bcftools - /usr/local/bin/bcftools [17:44:55] Found samtools - /usr/local/bin/samtools [17:44:55] Found java - /usr/local/bin/java [17:44:55] Found snpEff - /usr/local/bin/snpEff [17:44:55] Found samclip - /usr/local/bin/samclip [17:44:55] Found seqtk - /usr/local/bin/seqtk [17:44:55] Found parallel - /usr/local/bin/parallel [17:44:55] Found freebayes - /usr/local/bin/freebayes [17:44:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:44:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:44:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:44:55] Found vcfuniq - /usr/local/bin/vcfuniq [17:44:55] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:44:55] Found gzip - /bin/gzip [17:44:55] Found vt - /usr/local/bin/vt [17:44:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:44:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:44:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:44:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:44:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:44:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:44:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:44:56] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:49:01] This is snippy 4.6.0
Show full stderr[17:49:01] This is snippy 4.6.0 [17:49:01] Written by Torsten Seemann [17:49:01] Obtained from https://github.com/tseemann/snippy [17:49:01] Detected operating system: linux [17:49:01] Enabling bundled linux tools. [17:49:01] Found bwa - /usr/local/bin/bwa [17:49:01] Found bcftools - /usr/local/bin/bcftools [17:49:01] Found samtools - /usr/local/bin/samtools [17:49:01] Found java - /usr/local/bin/java [17:49:01] Found snpEff - /usr/local/bin/snpEff [17:49:01] Found samclip - /usr/local/bin/samclip [17:49:01] Found seqtk - /usr/local/bin/seqtk [17:49:01] Found parallel - /usr/local/bin/parallel [17:49:01] Found freebayes - /usr/local/bin/freebayes [17:49:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:49:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:49:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:49:01] Found vcfuniq - /usr/local/bin/vcfuniq [17:49:01] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:49:01] Found gzip - /bin/gzip [17:49:01] Found vt - /usr/local/bin/vt [17:49:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:49:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:49:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:49:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:49:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:49:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:49:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:49:01] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:55:17] This is snippy 4.6.0
Show full stderr[17:55:17] This is snippy 4.6.0 [17:55:17] Written by Torsten Seemann [17:55:17] Obtained from https://github.com/tseemann/snippy [17:55:17] Detected operating system: linux [17:55:17] Enabling bundled linux tools. [17:55:17] Found bwa - /usr/local/bin/bwa [17:55:17] Found bcftools - /usr/local/bin/bcftools [17:55:17] Found samtools - /usr/local/bin/samtools [17:55:17] Found java - /usr/local/bin/java [17:55:17] Found snpEff - /usr/local/bin/snpEff [17:55:17] Found samclip - /usr/local/bin/samclip [17:55:17] Found seqtk - /usr/local/bin/seqtk [17:55:17] Found parallel - /usr/local/bin/parallel [17:55:17] Found freebayes - /usr/local/bin/freebayes [17:55:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:55:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:55:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:55:17] Found vcfuniq - /usr/local/bin/vcfuniq [17:55:17] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:55:17] Found gzip - /bin/gzip [17:55:17] Found vt - /usr/local/bin/vt [17:55:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:55:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:55:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:55:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:55:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:55:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:55:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:55:18] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:45:13] This is snippy 4.6.0
Show full stderr[17:45:13] This is snippy 4.6.0 [17:45:13] Written by Torsten Seemann [17:45:13] Obtained from https://github.com/tseemann/snippy [17:45:13] Detected operating system: linux [17:45:13] Enabling bundled linux tools. [17:45:13] Found bwa - /usr/local/bin/bwa [17:45:13] Found bcftools - /usr/local/bin/bcftools [17:45:13] Found samtools - /usr/local/bin/samtools [17:45:13] Found java - /usr/local/bin/java [17:45:13] Found snpEff - /usr/local/bin/snpEff [17:45:13] Found samclip - /usr/local/bin/samclip [17:45:13] Found seqtk - /usr/local/bin/seqtk [17:45:13] Found parallel - /usr/local/bin/parallel [17:45:13] Found freebayes - /usr/local/bin/freebayes [17:45:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:45:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:45:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:45:13] Found vcfuniq - /usr/local/bin/vcfuniq [17:45:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:45:13] Found gzip - /bin/gzip [17:45:13] Found vt - /usr/local/bin/vt [17:45:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:45:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:45:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:45:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:45:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:45:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:45:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:45:14] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:45:21] This is snippy 4.6.0
Show full stderr[17:45:21] This is snippy 4.6.0 [17:45:21] Written by Torsten Seemann [17:45:21] Obtained from https://github.com/tseemann/snippy [17:45:21] Detected operating system: linux [17:45:21] Enabling bundled linux tools. [17:45:21] Found bwa - /usr/local/bin/bwa [17:45:21] Found bcftools - /usr/local/bin/bcftools [17:45:21] Found samtools - /usr/local/bin/samtools [17:45:21] Found java - /usr/local/bin/java [17:45:21] Found snpEff - /usr/local/bin/snpEff [17:45:21] Found samclip - /usr/local/bin/samclip [17:45:21] Found seqtk - /usr/local/bin/seqtk [17:45:21] Found parallel - /usr/local/bin/parallel [17:45:21] Found freebayes - /usr/local/bin/freebayes [17:45:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:45:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:45:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:45:21] Found vcfuniq - /usr/local/bin/vcfuniq [17:45:21] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:45:21] Found gzip - /bin/gzip [17:45:21] Found vt - /usr/local/bin/vt [17:45:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:45:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:45:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:45:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:45:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:45:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:45:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:45:22] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:45:36] This is snippy 4.6.0
Show full stderr[17:45:36] This is snippy 4.6.0 [17:45:36] Written by Torsten Seemann [17:45:36] Obtained from https://github.com/tseemann/snippy [17:45:36] Detected operating system: linux [17:45:36] Enabling bundled linux tools. [17:45:36] Found bwa - /usr/local/bin/bwa [17:45:36] Found bcftools - /usr/local/bin/bcftools [17:45:36] Found samtools - /usr/local/bin/samtools [17:45:36] Found java - /usr/local/bin/java [17:45:36] Found snpEff - /usr/local/bin/snpEff [17:45:36] Found samclip - /usr/local/bin/samclip [17:45:36] Found seqtk - /usr/local/bin/seqtk [17:45:36] Found parallel - /usr/local/bin/parallel [17:45:36] Found freebayes - /usr/local/bin/freebayes [17:45:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:45:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:45:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:45:36] Found vcfuniq - /usr/local/bin/vcfuniq [17:45:36] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:45:36] Found gzip - /bin/gzip [17:45:36] Found vt - /usr/local/bin/vt [17:45:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:45:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:45:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:45:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:45:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:45:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:45:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:45:37] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:45:42] This is snippy 4.6.0
Show full stderr[17:45:42] This is snippy 4.6.0 [17:45:42] Written by Torsten Seemann [17:45:42] Obtained from https://github.com/tseemann/snippy [17:45:42] Detected operating system: linux [17:45:42] Enabling bundled linux tools. [17:45:42] Found bwa - /usr/local/bin/bwa [17:45:42] Found bcftools - /usr/local/bin/bcftools [17:45:42] Found samtools - /usr/local/bin/samtools [17:45:42] Found java - /usr/local/bin/java [17:45:42] Found snpEff - /usr/local/bin/snpEff [17:45:42] Found samclip - /usr/local/bin/samclip [17:45:42] Found seqtk - /usr/local/bin/seqtk [17:45:42] Found parallel - /usr/local/bin/parallel [17:45:42] Found freebayes - /usr/local/bin/freebayes [17:45:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:45:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:45:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:45:42] Found vcfuniq - /usr/local/bin/vcfuniq [17:45:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:45:42] Found gzip - /bin/gzip [17:45:42] Found vt - /usr/local/bin/vt [17:45:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:45:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:45:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:45:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:45:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:45:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:45:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:45:43] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:45:51] This is snippy 4.6.0
Show full stderr[17:45:51] This is snippy 4.6.0 [17:45:51] Written by Torsten Seemann [17:45:51] Obtained from https://github.com/tseemann/snippy [17:45:51] Detected operating system: linux [17:45:51] Enabling bundled linux tools. [17:45:51] Found bwa - /usr/local/bin/bwa [17:45:51] Found bcftools - /usr/local/bin/bcftools [17:45:51] Found samtools - /usr/local/bin/samtools [17:45:51] Found java - /usr/local/bin/java [17:45:51] Found snpEff - /usr/local/bin/snpEff [17:45:51] Found samclip - /usr/local/bin/samclip [17:45:51] Found seqtk - /usr/local/bin/seqtk [17:45:51] Found parallel - /usr/local/bin/parallel [17:45:51] Found freebayes - /usr/local/bin/freebayes [17:45:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:45:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:45:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:45:51] Found vcfuniq - /usr/local/bin/vcfuniq [17:45:51] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:45:51] Found gzip - /bin/gzip [17:45:51] Found vt - /usr/local/bin/vt [17:45:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:45:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:45:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:45:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:45:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:45:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:45:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:45:52] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:46:00] This is snippy 4.6.0
Show full stderr[17:46:00] This is snippy 4.6.0 [17:46:00] Written by Torsten Seemann [17:46:00] Obtained from https://github.com/tseemann/snippy [17:46:00] Detected operating system: linux [17:46:00] Enabling bundled linux tools. [17:46:00] Found bwa - /usr/local/bin/bwa [17:46:00] Found bcftools - /usr/local/bin/bcftools [17:46:00] Found samtools - /usr/local/bin/samtools [17:46:00] Found java - /usr/local/bin/java [17:46:00] Found snpEff - /usr/local/bin/snpEff [17:46:00] Found samclip - /usr/local/bin/samclip [17:46:00] Found seqtk - /usr/local/bin/seqtk [17:46:00] Found parallel - /usr/local/bin/parallel [17:46:00] Found freebayes - /usr/local/bin/freebayes [17:46:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:46:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:46:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:46:00] Found vcfuniq - /usr/local/bin/vcfuniq [17:46:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:46:00] Found gzip - /bin/gzip [17:46:00] Found vt - /usr/local/bin/vt [17:46:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:46:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:46:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:46:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:46:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:46:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:46:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:46:01] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:46:14] This is snippy 4.6.0
Show full stderr[17:46:14] This is snippy 4.6.0 [17:46:14] Written by Torsten Seemann [17:46:14] Obtained from https://github.com/tseemann/snippy [17:46:14] Detected operating system: linux [17:46:14] Enabling bundled linux tools. [17:46:14] Found bwa - /usr/local/bin/bwa [17:46:14] Found bcftools - /usr/local/bin/bcftools [17:46:14] Found samtools - /usr/local/bin/samtools [17:46:14] Found java - /usr/local/bin/java [17:46:14] Found snpEff - /usr/local/bin/snpEff [17:46:14] Found samclip - /usr/local/bin/samclip [17:46:14] Found seqtk - /usr/local/bin/seqtk [17:46:14] Found parallel - /usr/local/bin/parallel [17:46:14] Found freebayes - /usr/local/bin/freebayes [17:46:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:46:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:46:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:46:14] Found vcfuniq - /usr/local/bin/vcfuniq [17:46:14] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:46:14] Found gzip - /bin/gzip [17:46:14] Found vt - /usr/local/bin/vt [17:46:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:46:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:46:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:46:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:46:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:46:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:46:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:46:16] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:46:12] This is snippy 4.6.0
Show full stderr[17:46:12] This is snippy 4.6.0 [17:46:12] Written by Torsten Seemann [17:46:12] Obtained from https://github.com/tseemann/snippy [17:46:12] Detected operating system: linux [17:46:12] Enabling bundled linux tools. [17:46:12] Found bwa - /usr/local/bin/bwa [17:46:12] Found bcftools - /usr/local/bin/bcftools [17:46:12] Found samtools - /usr/local/bin/samtools [17:46:12] Found java - /usr/local/bin/java [17:46:12] Found snpEff - /usr/local/bin/snpEff [17:46:12] Found samclip - /usr/local/bin/samclip [17:46:12] Found seqtk - /usr/local/bin/seqtk [17:46:12] Found parallel - /usr/local/bin/parallel [17:46:12] Found freebayes - /usr/local/bin/freebayes [17:46:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:46:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:46:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:46:12] Found vcfuniq - /usr/local/bin/vcfuniq [17:46:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:46:12] Found gzip - /bin/gzip [17:46:12] Found vt - /usr/local/bin/vt [17:46:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:46:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:46:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:46:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:46:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:46:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:46:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:46:13] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:46:43] This is snippy 4.6.0
Show full stderr[17:46:43] This is snippy 4.6.0 [17:46:43] Written by Torsten Seemann [17:46:43] Obtained from https://github.com/tseemann/snippy [17:46:43] Detected operating system: linux [17:46:43] Enabling bundled linux tools. [17:46:43] Found bwa - /usr/local/bin/bwa [17:46:43] Found bcftools - /usr/local/bin/bcftools [17:46:43] Found samtools - /usr/local/bin/samtools [17:46:43] Found java - /usr/local/bin/java [17:46:43] Found snpEff - /usr/local/bin/snpEff [17:46:43] Found samclip - /usr/local/bin/samclip [17:46:43] Found seqtk - /usr/local/bin/seqtk [17:46:43] Found parallel - /usr/local/bin/parallel [17:46:43] Found freebayes - /usr/local/bin/freebayes [17:46:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:46:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:46:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:46:43] Found vcfuniq - /usr/local/bin/vcfuniq [17:46:44] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:46:44] Found gzip - /bin/gzip [17:46:44] Found vt - /usr/local/bin/vt [17:46:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:46:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:46:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:46:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:46:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:46:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:46:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:46:45] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:46:36] This is snippy 4.6.0
Show full stderr[17:46:36] This is snippy 4.6.0 [17:46:36] Written by Torsten Seemann [17:46:36] Obtained from https://github.com/tseemann/snippy [17:46:36] Detected operating system: linux [17:46:36] Enabling bundled linux tools. [17:46:36] Found bwa - /usr/local/bin/bwa [17:46:36] Found bcftools - /usr/local/bin/bcftools [17:46:36] Found samtools - /usr/local/bin/samtools [17:46:36] Found java - /usr/local/bin/java [17:46:36] Found snpEff - /usr/local/bin/snpEff [17:46:36] Found samclip - /usr/local/bin/samclip [17:46:36] Found seqtk - /usr/local/bin/seqtk [17:46:36] Found parallel - /usr/local/bin/parallel [17:46:36] Found freebayes - /usr/local/bin/freebayes [17:46:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:46:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:46:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:46:36] Found vcfuniq - /usr/local/bin/vcfuniq [17:46:36] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:46:36] Found gzip - /bin/gzip [17:46:36] Found vt - /usr/local/bin/vt [17:46:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:46:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:46:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:46:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:46:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:46:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:46:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:46:37] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:46:42] This is snippy 4.6.0
Show full stderr[17:46:42] This is snippy 4.6.0 [17:46:42] Written by Torsten Seemann [17:46:42] Obtained from https://github.com/tseemann/snippy [17:46:42] Detected operating system: linux [17:46:42] Enabling bundled linux tools. [17:46:42] Found bwa - /usr/local/bin/bwa [17:46:42] Found bcftools - /usr/local/bin/bcftools [17:46:42] Found samtools - /usr/local/bin/samtools [17:46:42] Found java - /usr/local/bin/java [17:46:42] Found snpEff - /usr/local/bin/snpEff [17:46:42] Found samclip - /usr/local/bin/samclip [17:46:42] Found seqtk - /usr/local/bin/seqtk [17:46:42] Found parallel - /usr/local/bin/parallel [17:46:42] Found freebayes - /usr/local/bin/freebayes [17:46:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:46:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:46:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:46:42] Found vcfuniq - /usr/local/bin/vcfuniq [17:46:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:46:42] Found gzip - /bin/gzip [17:46:42] Found vt - /usr/local/bin/vt [17:46:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:46:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:46:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:46:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:46:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:46:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:46:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:46:43] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:46:51] This is snippy 4.6.0
Show full stderr[17:46:51] This is snippy 4.6.0 [17:46:51] Written by Torsten Seemann [17:46:51] Obtained from https://github.com/tseemann/snippy [17:46:51] Detected operating system: linux [17:46:51] Enabling bundled linux tools. [17:46:51] Found bwa - /usr/local/bin/bwa [17:46:51] Found bcftools - /usr/local/bin/bcftools [17:46:51] Found samtools - /usr/local/bin/samtools [17:46:51] Found java - /usr/local/bin/java [17:46:51] Found snpEff - /usr/local/bin/snpEff [17:46:51] Found samclip - /usr/local/bin/samclip [17:46:51] Found seqtk - /usr/local/bin/seqtk [17:46:51] Found parallel - /usr/local/bin/parallel [17:46:51] Found freebayes - /usr/local/bin/freebayes [17:46:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:46:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:46:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:46:51] Found vcfuniq - /usr/local/bin/vcfuniq [17:46:51] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:46:51] Found gzip - /bin/gzip [17:46:51] Found vt - /usr/local/bin/vt [17:46:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:46:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:46:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:46:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:46:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:46:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:46:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:46:52] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:46:59] This is snippy 4.6.0
Show full stderr[17:46:59] This is snippy 4.6.0 [17:46:59] Written by Torsten Seemann [17:46:59] Obtained from https://github.com/tseemann/snippy [17:46:59] Detected operating system: linux [17:46:59] Enabling bundled linux tools. [17:46:59] Found bwa - /usr/local/bin/bwa [17:46:59] Found bcftools - /usr/local/bin/bcftools [17:46:59] Found samtools - /usr/local/bin/samtools [17:46:59] Found java - /usr/local/bin/java [17:46:59] Found snpEff - /usr/local/bin/snpEff [17:46:59] Found samclip - /usr/local/bin/samclip [17:46:59] Found seqtk - /usr/local/bin/seqtk [17:46:59] Found parallel - /usr/local/bin/parallel [17:46:59] Found freebayes - /usr/local/bin/freebayes [17:46:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:46:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:46:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:46:59] Found vcfuniq - /usr/local/bin/vcfuniq [17:46:59] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:46:59] Found gzip - /bin/gzip [17:46:59] Found vt - /usr/local/bin/vt [17:46:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:46:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:46:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:46:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:46:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:47:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:47:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:47:00] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:47:13] This is snippy 4.6.0
Show full stderr[17:47:13] This is snippy 4.6.0 [17:47:13] Written by Torsten Seemann [17:47:13] Obtained from https://github.com/tseemann/snippy [17:47:13] Detected operating system: linux [17:47:13] Enabling bundled linux tools. [17:47:13] Found bwa - /usr/local/bin/bwa [17:47:13] Found bcftools - /usr/local/bin/bcftools [17:47:13] Found samtools - /usr/local/bin/samtools [17:47:13] Found java - /usr/local/bin/java [17:47:13] Found snpEff - /usr/local/bin/snpEff [17:47:13] Found samclip - /usr/local/bin/samclip [17:47:13] Found seqtk - /usr/local/bin/seqtk [17:47:13] Found parallel - /usr/local/bin/parallel [17:47:13] Found freebayes - /usr/local/bin/freebayes [17:47:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:47:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:47:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:47:13] Found vcfuniq - /usr/local/bin/vcfuniq [17:47:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:47:13] Found gzip - /bin/gzip [17:47:13] Found vt - /usr/local/bin/vt [17:47:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:47:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:47:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:47:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:47:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:47:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:47:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:47:15] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:47:20] This is snippy 4.6.0
Show full stderr[17:47:20] This is snippy 4.6.0 [17:47:20] Written by Torsten Seemann [17:47:20] Obtained from https://github.com/tseemann/snippy [17:47:20] Detected operating system: linux [17:47:20] Enabling bundled linux tools. [17:47:20] Found bwa - /usr/local/bin/bwa [17:47:20] Found bcftools - /usr/local/bin/bcftools [17:47:20] Found samtools - /usr/local/bin/samtools [17:47:20] Found java - /usr/local/bin/java [17:47:20] Found snpEff - /usr/local/bin/snpEff [17:47:20] Found samclip - /usr/local/bin/samclip [17:47:20] Found seqtk - /usr/local/bin/seqtk [17:47:20] Found parallel - /usr/local/bin/parallel [17:47:20] Found freebayes - /usr/local/bin/freebayes [17:47:20] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:47:20] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:47:20] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:47:20] Found vcfuniq - /usr/local/bin/vcfuniq [17:47:20] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:47:20] Found gzip - /bin/gzip [17:47:20] Found vt - /usr/local/bin/vt [17:47:20] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:47:20] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:47:20] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:47:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:47:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:47:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:47:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:47:22] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:47:24] This is snippy 4.6.0
Show full stderr[17:47:24] This is snippy 4.6.0 [17:47:24] Written by Torsten Seemann [17:47:24] Obtained from https://github.com/tseemann/snippy [17:47:24] Detected operating system: linux [17:47:24] Enabling bundled linux tools. [17:47:24] Found bwa - /usr/local/bin/bwa [17:47:24] Found bcftools - /usr/local/bin/bcftools [17:47:24] Found samtools - /usr/local/bin/samtools [17:47:24] Found java - /usr/local/bin/java [17:47:24] Found snpEff - /usr/local/bin/snpEff [17:47:24] Found samclip - /usr/local/bin/samclip [17:47:24] Found seqtk - /usr/local/bin/seqtk [17:47:24] Found parallel - /usr/local/bin/parallel [17:47:24] Found freebayes - /usr/local/bin/freebayes [17:47:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:47:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:47:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:47:24] Found vcfuniq - /usr/local/bin/vcfuniq [17:47:24] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:47:24] Found gzip - /bin/gzip [17:47:24] Found vt - /usr/local/bin/vt [17:47:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:47:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:47:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:47:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:47:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:47:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:47:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:47:25] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:42:58] This is snippy 4.6.0
Show full stderr[17:42:58] This is snippy 4.6.0 [17:42:58] Written by Torsten Seemann [17:42:58] Obtained from https://github.com/tseemann/snippy [17:42:58] Detected operating system: linux [17:42:58] Enabling bundled linux tools. [17:42:58] Found bwa - /usr/local/bin/bwa [17:42:58] Found bcftools - /usr/local/bin/bcftools [17:42:58] Found samtools - /usr/local/bin/samtools [17:42:58] Found java - /usr/local/bin/java [17:42:58] Found snpEff - /usr/local/bin/snpEff [17:42:58] Found samclip - /usr/local/bin/samclip [17:42:58] Found seqtk - /usr/local/bin/seqtk [17:42:58] Found parallel - /usr/local/bin/parallel [17:42:58] Found freebayes - /usr/local/bin/freebayes [17:42:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:42:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:42:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:42:58] Found vcfuniq - /usr/local/bin/vcfuniq [17:42:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:42:58] Found gzip - /bin/gzip [17:42:58] Found vt - /usr/local/bin/vt [17:42:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:42:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:42:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:42:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:42:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:42:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:42:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:42:59] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:44:16] This is snippy 4.6.0
Show full stderr[17:44:16] This is snippy 4.6.0 [17:44:16] Written by Torsten Seemann [17:44:16] Obtained from https://github.com/tseemann/snippy [17:44:16] Detected operating system: linux [17:44:16] Enabling bundled linux tools. [17:44:16] Found bwa - /usr/local/bin/bwa [17:44:16] Found bcftools - /usr/local/bin/bcftools [17:44:16] Found samtools - /usr/local/bin/samtools [17:44:16] Found java - /usr/local/bin/java [17:44:16] Found snpEff - /usr/local/bin/snpEff [17:44:16] Found samclip - /usr/local/bin/samclip [17:44:16] Found seqtk - /usr/local/bin/seqtk [17:44:16] Found parallel - /usr/local/bin/parallel [17:44:16] Found freebayes - /usr/local/bin/freebayes [17:44:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:44:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:44:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:44:16] Found vcfuniq - /usr/local/bin/vcfuniq [17:44:16] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:44:16] Found gzip - /bin/gzip [17:44:16] Found vt - /usr/local/bin/vt [17:44:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:44:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:44:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:44:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:44:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:44:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:44:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:44:17] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:45:27] This is snippy 4.6.0
Show full stderr[17:45:27] This is snippy 4.6.0 [17:45:27] Written by Torsten Seemann [17:45:27] Obtained from https://github.com/tseemann/snippy [17:45:27] Detected operating system: linux [17:45:27] Enabling bundled linux tools. [17:45:27] Found bwa - /usr/local/bin/bwa [17:45:27] Found bcftools - /usr/local/bin/bcftools [17:45:27] Found samtools - /usr/local/bin/samtools [17:45:27] Found java - /usr/local/bin/java [17:45:27] Found snpEff - /usr/local/bin/snpEff [17:45:27] Found samclip - /usr/local/bin/samclip [17:45:27] Found seqtk - /usr/local/bin/seqtk [17:45:27] Found parallel - /usr/local/bin/parallel [17:45:27] Found freebayes - /usr/local/bin/freebayes [17:45:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:45:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:45:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:45:27] Found vcfuniq - /usr/local/bin/vcfuniq [17:45:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:45:27] Found gzip - /bin/gzip [17:45:27] Found vt - /usr/local/bin/vt [17:45:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:45:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:45:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:45:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:45:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:45:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:45:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:45:28] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:45:33] This is snippy 4.6.0
Show full stderr[17:45:33] This is snippy 4.6.0 [17:45:33] Written by Torsten Seemann [17:45:33] Obtained from https://github.com/tseemann/snippy [17:45:33] Detected operating system: linux [17:45:33] Enabling bundled linux tools. [17:45:33] Found bwa - /usr/local/bin/bwa [17:45:33] Found bcftools - /usr/local/bin/bcftools [17:45:33] Found samtools - /usr/local/bin/samtools [17:45:33] Found java - /usr/local/bin/java [17:45:33] Found snpEff - /usr/local/bin/snpEff [17:45:33] Found samclip - /usr/local/bin/samclip [17:45:33] Found seqtk - /usr/local/bin/seqtk [17:45:33] Found parallel - /usr/local/bin/parallel [17:45:33] Found freebayes - /usr/local/bin/freebayes [17:45:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:45:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:45:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:45:33] Found vcfuniq - /usr/local/bin/vcfuniq [17:45:33] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:45:33] Found gzip - /bin/gzip [17:45:33] Found vt - /usr/local/bin/vt [17:45:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:45:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:45:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:45:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:45:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:45:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:45:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:45:34] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:45:48] This is snippy 4.6.0
Show full stderr[17:45:48] This is snippy 4.6.0 [17:45:48] Written by Torsten Seemann [17:45:48] Obtained from https://github.com/tseemann/snippy [17:45:48] Detected operating system: linux [17:45:48] Enabling bundled linux tools. [17:45:48] Found bwa - /usr/local/bin/bwa [17:45:48] Found bcftools - /usr/local/bin/bcftools [17:45:48] Found samtools - /usr/local/bin/samtools [17:45:48] Found java - /usr/local/bin/java [17:45:48] Found snpEff - /usr/local/bin/snpEff [17:45:48] Found samclip - /usr/local/bin/samclip [17:45:48] Found seqtk - /usr/local/bin/seqtk [17:45:48] Found parallel - /usr/local/bin/parallel [17:45:48] Found freebayes - /usr/local/bin/freebayes [17:45:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:45:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:45:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:45:48] Found vcfuniq - /usr/local/bin/vcfuniq [17:45:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:45:48] Found gzip - /bin/gzip [17:45:48] Found vt - /usr/local/bin/vt [17:45:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:45:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:45:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:45:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:45:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:45:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:45:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:45:49] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:46:04] This is snippy 4.6.0
Show full stderr[17:46:04] This is snippy 4.6.0 [17:46:04] Written by Torsten Seemann [17:46:04] Obtained from https://github.com/tseemann/snippy [17:46:04] Detected operating system: linux [17:46:04] Enabling bundled linux tools. [17:46:04] Found bwa - /usr/local/bin/bwa [17:46:04] Found bcftools - /usr/local/bin/bcftools [17:46:04] Found samtools - /usr/local/bin/samtools [17:46:04] Found java - /usr/local/bin/java [17:46:04] Found snpEff - /usr/local/bin/snpEff [17:46:04] Found samclip - /usr/local/bin/samclip [17:46:04] Found seqtk - /usr/local/bin/seqtk [17:46:04] Found parallel - /usr/local/bin/parallel [17:46:04] Found freebayes - /usr/local/bin/freebayes [17:46:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:46:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:46:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:46:05] Found vcfuniq - /usr/local/bin/vcfuniq [17:46:05] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:46:05] Found gzip - /bin/gzip [17:46:05] Found vt - /usr/local/bin/vt [17:46:05] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:46:05] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:46:05] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:46:05] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:46:05] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:46:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:46:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:46:06] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:46:27] This is snippy 4.6.0
Show full stderr[17:46:27] This is snippy 4.6.0 [17:46:27] Written by Torsten Seemann [17:46:27] Obtained from https://github.com/tseemann/snippy [17:46:27] Detected operating system: linux [17:46:27] Enabling bundled linux tools. [17:46:27] Found bwa - /usr/local/bin/bwa [17:46:27] Found bcftools - /usr/local/bin/bcftools [17:46:27] Found samtools - /usr/local/bin/samtools [17:46:27] Found java - /usr/local/bin/java [17:46:27] Found snpEff - /usr/local/bin/snpEff [17:46:27] Found samclip - /usr/local/bin/samclip [17:46:27] Found seqtk - /usr/local/bin/seqtk [17:46:27] Found parallel - /usr/local/bin/parallel [17:46:27] Found freebayes - /usr/local/bin/freebayes [17:46:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:46:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:46:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:46:27] Found vcfuniq - /usr/local/bin/vcfuniq [17:46:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:46:27] Found gzip - /bin/gzip [17:46:27] Found vt - /usr/local/bin/vt [17:46:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:46:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:46:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:46:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:46:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:46:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:46:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:46:28] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:52:06] This is snippy 4.6.0
Show full stderr[17:52:06] This is snippy 4.6.0 [17:52:06] Written by Torsten Seemann [17:52:06] Obtained from https://github.com/tseemann/snippy [17:52:06] Detected operating system: linux [17:52:06] Enabling bundled linux tools. [17:52:06] Found bwa - /usr/local/bin/bwa [17:52:06] Found bcftools - /usr/local/bin/bcftools [17:52:06] Found samtools - /usr/local/bin/samtools [17:52:06] Found java - /usr/local/bin/java [17:52:06] Found snpEff - /usr/local/bin/snpEff [17:52:06] Found samclip - /usr/local/bin/samclip [17:52:06] Found seqtk - /usr/local/bin/seqtk [17:52:06] Found parallel - /usr/local/bin/parallel [17:52:06] Found freebayes - /usr/local/bin/freebayes [17:52:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:52:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:52:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:52:07] Found vcfuniq - /usr/local/bin/vcfuniq [17:52:07] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:52:07] Found gzip - /bin/gzip [17:52:07] Found vt - /usr/local/bin/vt [17:52:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:52:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:52:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:52:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:52:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:52:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:52:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:52:08] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:48:44] This is snippy 4.6.0
Show full stderr[17:48:44] This is snippy 4.6.0 [17:48:44] Written by Torsten Seemann [17:48:44] Obtained from https://github.com/tseemann/snippy [17:48:44] Detected operating system: linux [17:48:44] Enabling bundled linux tools. [17:48:44] Found bwa - /usr/local/bin/bwa [17:48:44] Found bcftools - /usr/local/bin/bcftools [17:48:44] Found samtools - /usr/local/bin/samtools [17:48:44] Found java - /usr/local/bin/java [17:48:44] Found snpEff - /usr/local/bin/snpEff [17:48:44] Found samclip - /usr/local/bin/samclip [17:48:44] Found seqtk - /usr/local/bin/seqtk [17:48:44] Found parallel - /usr/local/bin/parallel [17:48:44] Found freebayes - /usr/local/bin/freebayes [17:48:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:48:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:48:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:48:44] Found vcfuniq - /usr/local/bin/vcfuniq [17:48:44] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:48:44] Found gzip - /bin/gzip [17:48:44] Found vt - /usr/local/bin/vt [17:48:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:48:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:48:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:48:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:48:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:48:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:48:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:48:49] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:52:51] This is snippy 4.6.0
Show full stderr[17:52:51] This is snippy 4.6.0 [17:52:51] Written by Torsten Seemann [17:52:51] Obtained from https://github.com/tseemann/snippy [17:52:51] Detected operating system: linux [17:52:51] Enabling bundled linux tools. [17:52:51] Found bwa - /usr/local/bin/bwa [17:52:51] Found bcftools - /usr/local/bin/bcftools [17:52:51] Found samtools - /usr/local/bin/samtools [17:52:51] Found java - /usr/local/bin/java [17:52:51] Found snpEff - /usr/local/bin/snpEff [17:52:51] Found samclip - /usr/local/bin/samclip [17:52:51] Found seqtk - /usr/local/bin/seqtk [17:52:51] Found parallel - /usr/local/bin/parallel [17:52:51] Found freebayes - /usr/local/bin/freebayes [17:52:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:52:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:52:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:52:51] Found vcfuniq - /usr/local/bin/vcfuniq [17:52:51] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:52:51] Found gzip - /bin/gzip [17:52:51] Found vt - /usr/local/bin/vt [17:52:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:52:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:52:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:52:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:52:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:52:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:52:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:52:51] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:56:28] This is snippy 4.6.0
Show full stderr[17:56:28] This is snippy 4.6.0 [17:56:28] Written by Torsten Seemann [17:56:28] Obtained from https://github.com/tseemann/snippy [17:56:28] Detected operating system: linux [17:56:28] Enabling bundled linux tools. [17:56:28] Found bwa - /usr/local/bin/bwa [17:56:28] Found bcftools - /usr/local/bin/bcftools [17:56:28] Found samtools - /usr/local/bin/samtools [17:56:28] Found java - /usr/local/bin/java [17:56:28] Found snpEff - /usr/local/bin/snpEff [17:56:28] Found samclip - /usr/local/bin/samclip [17:56:28] Found seqtk - /usr/local/bin/seqtk [17:56:28] Found parallel - /usr/local/bin/parallel [17:56:28] Found freebayes - /usr/local/bin/freebayes [17:56:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:56:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:56:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:56:28] Found vcfuniq - /usr/local/bin/vcfuniq [17:56:28] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:56:28] Found gzip - /bin/gzip [17:56:28] Found vt - /usr/local/bin/vt [17:56:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:56:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:56:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:56:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:56:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:56:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:56:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:56:29] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:51:28] This is snippy 4.6.0
Show full stderr[17:51:28] This is snippy 4.6.0 [17:51:28] Written by Torsten Seemann [17:51:28] Obtained from https://github.com/tseemann/snippy [17:51:28] Detected operating system: linux [17:51:28] Enabling bundled linux tools. [17:51:28] Found bwa - /usr/local/bin/bwa [17:51:28] Found bcftools - /usr/local/bin/bcftools [17:51:28] Found samtools - /usr/local/bin/samtools [17:51:28] Found java - /usr/local/bin/java [17:51:29] Found snpEff - /usr/local/bin/snpEff [17:51:29] Found samclip - /usr/local/bin/samclip [17:51:29] Found seqtk - /usr/local/bin/seqtk [17:51:29] Found parallel - /usr/local/bin/parallel [17:51:29] Found freebayes - /usr/local/bin/freebayes [17:51:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:51:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:51:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:51:29] Found vcfuniq - /usr/local/bin/vcfuniq [17:51:29] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:51:29] Found gzip - /bin/gzip [17:51:29] Found vt - /usr/local/bin/vt [17:51:29] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:51:29] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:51:29] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:51:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:51:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:51:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:51:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:51:29] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:51:55] This is snippy 4.6.0
Show full stderr[17:51:55] This is snippy 4.6.0 [17:51:55] Written by Torsten Seemann [17:51:55] Obtained from https://github.com/tseemann/snippy [17:51:55] Detected operating system: linux [17:51:55] Enabling bundled linux tools. [17:51:55] Found bwa - /usr/local/bin/bwa [17:51:55] Found bcftools - /usr/local/bin/bcftools [17:51:55] Found samtools - /usr/local/bin/samtools [17:51:55] Found java - /usr/local/bin/java [17:51:55] Found snpEff - /usr/local/bin/snpEff [17:51:55] Found samclip - /usr/local/bin/samclip [17:51:55] Found seqtk - /usr/local/bin/seqtk [17:51:55] Found parallel - /usr/local/bin/parallel [17:51:55] Found freebayes - /usr/local/bin/freebayes [17:51:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:51:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:51:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:51:55] Found vcfuniq - /usr/local/bin/vcfuniq [17:51:55] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:51:55] Found gzip - /bin/gzip [17:51:55] Found vt - /usr/local/bin/vt [17:51:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:51:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:51:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:51:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:51:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:51:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:51:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:51:56] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:56:37] This is snippy 4.6.0
Show full stderr[17:56:37] This is snippy 4.6.0 [17:56:37] Written by Torsten Seemann [17:56:37] Obtained from https://github.com/tseemann/snippy [17:56:37] Detected operating system: linux [17:56:37] Enabling bundled linux tools. [17:56:37] Found bwa - /usr/local/bin/bwa [17:56:37] Found bcftools - /usr/local/bin/bcftools [17:56:37] Found samtools - /usr/local/bin/samtools [17:56:37] Found java - /usr/local/bin/java [17:56:37] Found snpEff - /usr/local/bin/snpEff [17:56:37] Found samclip - /usr/local/bin/samclip [17:56:37] Found seqtk - /usr/local/bin/seqtk [17:56:37] Found parallel - /usr/local/bin/parallel [17:56:37] Found freebayes - /usr/local/bin/freebayes [17:56:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:56:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:56:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:56:37] Found vcfuniq - /usr/local/bin/vcfuniq [17:56:37] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:56:37] Found gzip - /bin/gzip [17:56:37] Found vt - /usr/local/bin/vt [17:56:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:56:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:56:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:56:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:56:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:56:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:56:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:56:38] Please supply a reference FASTA/GBK/EMBL file with --reference
1[17:52:37] This is snippy 4.6.0
Show full stderr[17:52:37] This is snippy 4.6.0 [17:52:37] Written by Torsten Seemann [17:52:37] Obtained from https://github.com/tseemann/snippy [17:52:37] Detected operating system: linux [17:52:37] Enabling bundled linux tools. [17:52:37] Found bwa - /usr/local/bin/bwa [17:52:37] Found bcftools - /usr/local/bin/bcftools [17:52:37] Found samtools - /usr/local/bin/samtools [17:52:37] Found java - /usr/local/bin/java [17:52:37] Found snpEff - /usr/local/bin/snpEff [17:52:37] Found samclip - /usr/local/bin/samclip [17:52:37] Found seqtk - /usr/local/bin/seqtk [17:52:37] Found parallel - /usr/local/bin/parallel [17:52:37] Found freebayes - /usr/local/bin/freebayes [17:52:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:52:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:52:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:52:37] Found vcfuniq - /usr/local/bin/vcfuniq [17:52:37] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:52:37] Found gzip - /bin/gzip [17:52:37] Found vt - /usr/local/bin/vt [17:52:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:52:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:52:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:52:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:52:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:52:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:52:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:52:37] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:22:44] This is snippy 4.6.0
Show full stderr[00:22:44] This is snippy 4.6.0 [00:22:44] Written by Torsten Seemann [00:22:44] Obtained from https://github.com/tseemann/snippy [00:22:44] Detected operating system: linux [00:22:44] Enabling bundled linux tools. [00:22:44] Found bwa - /usr/local/bin/bwa [00:22:44] Found bcftools - /usr/local/bin/bcftools [00:22:44] Found samtools - /usr/local/bin/samtools [00:22:44] Found java - /usr/local/bin/java [00:22:44] Found snpEff - /usr/local/bin/snpEff [00:22:44] Found samclip - /usr/local/bin/samclip [00:22:44] Found seqtk - /usr/local/bin/seqtk [00:22:44] Found parallel - /usr/local/bin/parallel [00:22:44] Found freebayes - /usr/local/bin/freebayes [00:22:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:22:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:22:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:22:44] Found vcfuniq - /usr/local/bin/vcfuniq [00:22:44] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:22:44] Found gzip - /bin/gzip [00:22:44] Found vt - /usr/local/bin/vt [00:22:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:22:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:22:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:22:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:22:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:22:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:22:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:22:45] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:23:07] This is snippy 4.6.0
Show full stderr[00:23:07] This is snippy 4.6.0 [00:23:07] Written by Torsten Seemann [00:23:07] Obtained from https://github.com/tseemann/snippy [00:23:07] Detected operating system: linux [00:23:07] Enabling bundled linux tools. [00:23:07] Found bwa - /usr/local/bin/bwa [00:23:07] Found bcftools - /usr/local/bin/bcftools [00:23:07] Found samtools - /usr/local/bin/samtools [00:23:07] Found java - /usr/local/bin/java [00:23:07] Found snpEff - /usr/local/bin/snpEff [00:23:07] Found samclip - /usr/local/bin/samclip [00:23:07] Found seqtk - /usr/local/bin/seqtk [00:23:07] Found parallel - /usr/local/bin/parallel [00:23:07] Found freebayes - /usr/local/bin/freebayes [00:23:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:23:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:23:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:23:07] Found vcfuniq - /usr/local/bin/vcfuniq [00:23:07] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:23:07] Found gzip - /bin/gzip [00:23:07] Found vt - /usr/local/bin/vt [00:23:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:23:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:23:08] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:23:08] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:23:08] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:23:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:23:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:23:10] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:23:14] This is snippy 4.6.0
Show full stderr[00:23:14] This is snippy 4.6.0 [00:23:14] Written by Torsten Seemann [00:23:14] Obtained from https://github.com/tseemann/snippy [00:23:14] Detected operating system: linux [00:23:14] Enabling bundled linux tools. [00:23:14] Found bwa - /usr/local/bin/bwa [00:23:14] Found bcftools - /usr/local/bin/bcftools [00:23:14] Found samtools - /usr/local/bin/samtools [00:23:14] Found java - /usr/local/bin/java [00:23:14] Found snpEff - /usr/local/bin/snpEff [00:23:14] Found samclip - /usr/local/bin/samclip [00:23:14] Found seqtk - /usr/local/bin/seqtk [00:23:14] Found parallel - /usr/local/bin/parallel [00:23:14] Found freebayes - /usr/local/bin/freebayes [00:23:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:23:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:23:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:23:15] Found vcfuniq - /usr/local/bin/vcfuniq [00:23:15] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:23:15] Found gzip - /bin/gzip [00:23:15] Found vt - /usr/local/bin/vt [00:23:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:23:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:23:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:23:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:23:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:23:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:23:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:23:16] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:23:32] This is snippy 4.6.0
Show full stderr[00:23:32] This is snippy 4.6.0 [00:23:32] Written by Torsten Seemann [00:23:32] Obtained from https://github.com/tseemann/snippy [00:23:32] Detected operating system: linux [00:23:32] Enabling bundled linux tools. [00:23:32] Found bwa - /usr/local/bin/bwa [00:23:32] Found bcftools - /usr/local/bin/bcftools [00:23:32] Found samtools - /usr/local/bin/samtools [00:23:32] Found java - /usr/local/bin/java [00:23:32] Found snpEff - /usr/local/bin/snpEff [00:23:32] Found samclip - /usr/local/bin/samclip [00:23:32] Found seqtk - /usr/local/bin/seqtk [00:23:32] Found parallel - /usr/local/bin/parallel [00:23:32] Found freebayes - /usr/local/bin/freebayes [00:23:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:23:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:23:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:23:32] Found vcfuniq - /usr/local/bin/vcfuniq [00:23:32] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:23:32] Found gzip - /bin/gzip [00:23:32] Found vt - /usr/local/bin/vt [00:23:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:23:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:23:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:23:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:23:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:23:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:23:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:23:33] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:23:54] This is snippy 4.6.0
Show full stderr[00:23:54] This is snippy 4.6.0 [00:23:54] Written by Torsten Seemann [00:23:54] Obtained from https://github.com/tseemann/snippy [00:23:54] Detected operating system: linux [00:23:54] Enabling bundled linux tools. [00:23:54] Found bwa - /usr/local/bin/bwa [00:23:54] Found bcftools - /usr/local/bin/bcftools [00:23:54] Found samtools - /usr/local/bin/samtools [00:23:54] Found java - /usr/local/bin/java [00:23:54] Found snpEff - /usr/local/bin/snpEff [00:23:54] Found samclip - /usr/local/bin/samclip [00:23:54] Found seqtk - /usr/local/bin/seqtk [00:23:54] Found parallel - /usr/local/bin/parallel [00:23:54] Found freebayes - /usr/local/bin/freebayes [00:23:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:23:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:23:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:23:54] Found vcfuniq - /usr/local/bin/vcfuniq [00:23:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:23:54] Found gzip - /bin/gzip [00:23:54] Found vt - /usr/local/bin/vt [00:23:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:23:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:23:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:23:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:23:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:23:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:23:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:23:55] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:25:24] This is snippy 4.6.0
Show full stderr[00:25:24] This is snippy 4.6.0 [00:25:24] Written by Torsten Seemann [00:25:24] Obtained from https://github.com/tseemann/snippy [00:25:24] Detected operating system: linux [00:25:24] Enabling bundled linux tools. [00:25:24] Found bwa - /usr/local/bin/bwa [00:25:24] Found bcftools - /usr/local/bin/bcftools [00:25:24] Found samtools - /usr/local/bin/samtools [00:25:24] Found java - /usr/local/bin/java [00:25:24] Found snpEff - /usr/local/bin/snpEff [00:25:24] Found samclip - /usr/local/bin/samclip [00:25:24] Found seqtk - /usr/local/bin/seqtk [00:25:24] Found parallel - /usr/local/bin/parallel [00:25:24] Found freebayes - /usr/local/bin/freebayes [00:25:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:25:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:25:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:25:24] Found vcfuniq - /usr/local/bin/vcfuniq [00:25:24] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:25:24] Found gzip - /bin/gzip [00:25:24] Found vt - /usr/local/bin/vt [00:25:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:25:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:25:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:25:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:25:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:25:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:25:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:25:26] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:24:30] This is snippy 4.6.0
Show full stderr[00:24:30] This is snippy 4.6.0 [00:24:30] Written by Torsten Seemann [00:24:30] Obtained from https://github.com/tseemann/snippy [00:24:30] Detected operating system: linux [00:24:30] Enabling bundled linux tools. [00:24:30] Found bwa - /usr/local/bin/bwa [00:24:30] Found bcftools - /usr/local/bin/bcftools [00:24:30] Found samtools - /usr/local/bin/samtools [00:24:30] Found java - /usr/local/bin/java [00:24:30] Found snpEff - /usr/local/bin/snpEff [00:24:30] Found samclip - /usr/local/bin/samclip [00:24:30] Found seqtk - /usr/local/bin/seqtk [00:24:30] Found parallel - /usr/local/bin/parallel [00:24:30] Found freebayes - /usr/local/bin/freebayes [00:24:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:24:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:24:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:24:31] Found vcfuniq - /usr/local/bin/vcfuniq [00:24:31] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:24:31] Found gzip - /bin/gzip [00:24:31] Found vt - /usr/local/bin/vt [00:24:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:24:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:24:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:24:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:24:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:24:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:24:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:24:32] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:23:29] This is snippy 4.6.0
Show full stderr[00:23:29] This is snippy 4.6.0 [00:23:29] Written by Torsten Seemann [00:23:29] Obtained from https://github.com/tseemann/snippy [00:23:29] Detected operating system: linux [00:23:29] Enabling bundled linux tools. [00:23:29] Found bwa - /usr/local/bin/bwa [00:23:29] Found bcftools - /usr/local/bin/bcftools [00:23:29] Found samtools - /usr/local/bin/samtools [00:23:29] Found java - /usr/local/bin/java [00:23:29] Found snpEff - /usr/local/bin/snpEff [00:23:29] Found samclip - /usr/local/bin/samclip [00:23:29] Found seqtk - /usr/local/bin/seqtk [00:23:29] Found parallel - /usr/local/bin/parallel [00:23:29] Found freebayes - /usr/local/bin/freebayes [00:23:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:23:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:23:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:23:29] Found vcfuniq - /usr/local/bin/vcfuniq [00:23:29] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:23:29] Found gzip - /bin/gzip [00:23:29] Found vt - /usr/local/bin/vt [00:23:29] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:23:29] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:23:29] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:23:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:23:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:23:30] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:23:30] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:23:30] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:24:09] This is snippy 4.6.0
Show full stderr[00:24:09] This is snippy 4.6.0 [00:24:09] Written by Torsten Seemann [00:24:09] Obtained from https://github.com/tseemann/snippy [00:24:09] Detected operating system: linux [00:24:09] Enabling bundled linux tools. [00:24:09] Found bwa - /usr/local/bin/bwa [00:24:09] Found bcftools - /usr/local/bin/bcftools [00:24:09] Found samtools - /usr/local/bin/samtools [00:24:09] Found java - /usr/local/bin/java [00:24:09] Found snpEff - /usr/local/bin/snpEff [00:24:09] Found samclip - /usr/local/bin/samclip [00:24:09] Found seqtk - /usr/local/bin/seqtk [00:24:09] Found parallel - /usr/local/bin/parallel [00:24:09] Found freebayes - /usr/local/bin/freebayes [00:24:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:24:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:24:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:24:09] Found vcfuniq - /usr/local/bin/vcfuniq [00:24:09] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:24:09] Found gzip - /bin/gzip [00:24:09] Found vt - /usr/local/bin/vt [00:24:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:24:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:24:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:24:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:24:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:24:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:24:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:24:10] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:25:23] This is snippy 4.6.0
Show full stderr[00:25:23] This is snippy 4.6.0 [00:25:23] Written by Torsten Seemann [00:25:23] Obtained from https://github.com/tseemann/snippy [00:25:23] Detected operating system: linux [00:25:23] Enabling bundled linux tools. [00:25:23] Found bwa - /usr/local/bin/bwa [00:25:23] Found bcftools - /usr/local/bin/bcftools [00:25:23] Found samtools - /usr/local/bin/samtools [00:25:23] Found java - /usr/local/bin/java [00:25:23] Found snpEff - /usr/local/bin/snpEff [00:25:23] Found samclip - /usr/local/bin/samclip [00:25:23] Found seqtk - /usr/local/bin/seqtk [00:25:23] Found parallel - /usr/local/bin/parallel [00:25:23] Found freebayes - /usr/local/bin/freebayes [00:25:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:25:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:25:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:25:23] Found vcfuniq - /usr/local/bin/vcfuniq [00:25:23] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:25:23] Found gzip - /bin/gzip [00:25:23] Found vt - /usr/local/bin/vt [00:25:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:25:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:25:23] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:25:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:25:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:25:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:25:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:25:24] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:25:30] This is snippy 4.6.0
Show full stderr[00:25:30] This is snippy 4.6.0 [00:25:30] Written by Torsten Seemann [00:25:30] Obtained from https://github.com/tseemann/snippy [00:25:30] Detected operating system: linux [00:25:30] Enabling bundled linux tools. [00:25:30] Found bwa - /usr/local/bin/bwa [00:25:30] Found bcftools - /usr/local/bin/bcftools [00:25:30] Found samtools - /usr/local/bin/samtools [00:25:30] Found java - /usr/local/bin/java [00:25:30] Found snpEff - /usr/local/bin/snpEff [00:25:30] Found samclip - /usr/local/bin/samclip [00:25:30] Found seqtk - /usr/local/bin/seqtk [00:25:30] Found parallel - /usr/local/bin/parallel [00:25:30] Found freebayes - /usr/local/bin/freebayes [00:25:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:25:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:25:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:25:30] Found vcfuniq - /usr/local/bin/vcfuniq [00:25:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:25:30] Found gzip - /bin/gzip [00:25:30] Found vt - /usr/local/bin/vt [00:25:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:25:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:25:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:25:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:25:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:25:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:25:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:25:31] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:26:09] This is snippy 4.6.0
Show full stderr[00:26:09] This is snippy 4.6.0 [00:26:09] Written by Torsten Seemann [00:26:09] Obtained from https://github.com/tseemann/snippy [00:26:09] Detected operating system: linux [00:26:09] Enabling bundled linux tools. [00:26:09] Found bwa - /usr/local/bin/bwa [00:26:09] Found bcftools - /usr/local/bin/bcftools [00:26:09] Found samtools - /usr/local/bin/samtools [00:26:09] Found java - /usr/local/bin/java [00:26:10] Found snpEff - /usr/local/bin/snpEff [00:26:10] Found samclip - /usr/local/bin/samclip [00:26:10] Found seqtk - /usr/local/bin/seqtk [00:26:10] Found parallel - /usr/local/bin/parallel [00:26:10] Found freebayes - /usr/local/bin/freebayes [00:26:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:26:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:26:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:26:10] Found vcfuniq - /usr/local/bin/vcfuniq [00:26:10] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:26:10] Found gzip - /bin/gzip [00:26:10] Found vt - /usr/local/bin/vt [00:26:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:26:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:26:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:26:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:26:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:26:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:26:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:26:11] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:26:22] This is snippy 4.6.0
Show full stderr[00:26:22] This is snippy 4.6.0 [00:26:22] Written by Torsten Seemann [00:26:22] Obtained from https://github.com/tseemann/snippy [00:26:22] Detected operating system: linux [00:26:22] Enabling bundled linux tools. [00:26:22] Found bwa - /usr/local/bin/bwa [00:26:22] Found bcftools - /usr/local/bin/bcftools [00:26:22] Found samtools - /usr/local/bin/samtools [00:26:22] Found java - /usr/local/bin/java [00:26:22] Found snpEff - /usr/local/bin/snpEff [00:26:22] Found samclip - /usr/local/bin/samclip [00:26:22] Found seqtk - /usr/local/bin/seqtk [00:26:22] Found parallel - /usr/local/bin/parallel [00:26:22] Found freebayes - /usr/local/bin/freebayes [00:26:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:26:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:26:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:26:22] Found vcfuniq - /usr/local/bin/vcfuniq [00:26:22] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:26:22] Found gzip - /bin/gzip [00:26:22] Found vt - /usr/local/bin/vt [00:26:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:26:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:26:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:26:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:26:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:26:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:26:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:26:23] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:26:27] This is snippy 4.6.0
Show full stderr[00:26:27] This is snippy 4.6.0 [00:26:27] Written by Torsten Seemann [00:26:27] Obtained from https://github.com/tseemann/snippy [00:26:27] Detected operating system: linux [00:26:27] Enabling bundled linux tools. [00:26:27] Found bwa - /usr/local/bin/bwa [00:26:27] Found bcftools - /usr/local/bin/bcftools [00:26:27] Found samtools - /usr/local/bin/samtools [00:26:27] Found java - /usr/local/bin/java [00:26:27] Found snpEff - /usr/local/bin/snpEff [00:26:27] Found samclip - /usr/local/bin/samclip [00:26:27] Found seqtk - /usr/local/bin/seqtk [00:26:27] Found parallel - /usr/local/bin/parallel [00:26:27] Found freebayes - /usr/local/bin/freebayes [00:26:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:26:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:26:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:26:27] Found vcfuniq - /usr/local/bin/vcfuniq [00:26:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:26:27] Found gzip - /bin/gzip [00:26:27] Found vt - /usr/local/bin/vt [00:26:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:26:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:26:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:26:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:26:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:26:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:26:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:26:28] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:26:33] This is snippy 4.6.0
Show full stderr[00:26:33] This is snippy 4.6.0 [00:26:33] Written by Torsten Seemann [00:26:33] Obtained from https://github.com/tseemann/snippy [00:26:33] Detected operating system: linux [00:26:33] Enabling bundled linux tools. [00:26:33] Found bwa - /usr/local/bin/bwa [00:26:33] Found bcftools - /usr/local/bin/bcftools [00:26:33] Found samtools - /usr/local/bin/samtools [00:26:33] Found java - /usr/local/bin/java [00:26:33] Found snpEff - /usr/local/bin/snpEff [00:26:33] Found samclip - /usr/local/bin/samclip [00:26:33] Found seqtk - /usr/local/bin/seqtk [00:26:33] Found parallel - /usr/local/bin/parallel [00:26:33] Found freebayes - /usr/local/bin/freebayes [00:26:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:26:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:26:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:26:33] Found vcfuniq - /usr/local/bin/vcfuniq [00:26:33] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:26:33] Found gzip - /bin/gzip [00:26:33] Found vt - /usr/local/bin/vt [00:26:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:26:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:26:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:26:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:26:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:26:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:26:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:26:34] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:27:00] This is snippy 4.6.0
Show full stderr[00:27:00] This is snippy 4.6.0 [00:27:00] Written by Torsten Seemann [00:27:00] Obtained from https://github.com/tseemann/snippy [00:27:00] Detected operating system: linux [00:27:00] Enabling bundled linux tools. [00:27:00] Found bwa - /usr/local/bin/bwa [00:27:00] Found bcftools - /usr/local/bin/bcftools [00:27:00] Found samtools - /usr/local/bin/samtools [00:27:00] Found java - /usr/local/bin/java [00:27:00] Found snpEff - /usr/local/bin/snpEff [00:27:00] Found samclip - /usr/local/bin/samclip [00:27:00] Found seqtk - /usr/local/bin/seqtk [00:27:00] Found parallel - /usr/local/bin/parallel [00:27:00] Found freebayes - /usr/local/bin/freebayes [00:27:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:27:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:27:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:27:00] Found vcfuniq - /usr/local/bin/vcfuniq [00:27:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:27:00] Found gzip - /bin/gzip [00:27:00] Found vt - /usr/local/bin/vt [00:27:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:27:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:27:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:27:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:27:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:27:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:27:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:27:01] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:23:16] This is snippy 4.6.0
Show full stderr[00:23:16] This is snippy 4.6.0 [00:23:16] Written by Torsten Seemann [00:23:16] Obtained from https://github.com/tseemann/snippy [00:23:16] Detected operating system: linux [00:23:16] Enabling bundled linux tools. [00:23:16] Found bwa - /usr/local/bin/bwa [00:23:16] Found bcftools - /usr/local/bin/bcftools [00:23:17] Found samtools - /usr/local/bin/samtools [00:23:17] Found java - /usr/local/bin/java [00:23:17] Found snpEff - /usr/local/bin/snpEff [00:23:17] Found samclip - /usr/local/bin/samclip [00:23:17] Found seqtk - /usr/local/bin/seqtk [00:23:17] Found parallel - /usr/local/bin/parallel [00:23:17] Found freebayes - /usr/local/bin/freebayes [00:23:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:23:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:23:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:23:17] Found vcfuniq - /usr/local/bin/vcfuniq [00:23:17] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:23:17] Found gzip - /bin/gzip [00:23:17] Found vt - /usr/local/bin/vt [00:23:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:23:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:23:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:23:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:23:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:23:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:23:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:23:18] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:23:13] This is snippy 4.6.0
Show full stderr[00:23:13] This is snippy 4.6.0 [00:23:13] Written by Torsten Seemann [00:23:13] Obtained from https://github.com/tseemann/snippy [00:23:13] Detected operating system: linux [00:23:13] Enabling bundled linux tools. [00:23:13] Found bwa - /usr/local/bin/bwa [00:23:13] Found bcftools - /usr/local/bin/bcftools [00:23:13] Found samtools - /usr/local/bin/samtools [00:23:13] Found java - /usr/local/bin/java [00:23:13] Found snpEff - /usr/local/bin/snpEff [00:23:13] Found samclip - /usr/local/bin/samclip [00:23:13] Found seqtk - /usr/local/bin/seqtk [00:23:13] Found parallel - /usr/local/bin/parallel [00:23:13] Found freebayes - /usr/local/bin/freebayes [00:23:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:23:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:23:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:23:13] Found vcfuniq - /usr/local/bin/vcfuniq [00:23:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:23:13] Found gzip - /bin/gzip [00:23:13] Found vt - /usr/local/bin/vt [00:23:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:23:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:23:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:23:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:23:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:23:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:23:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:23:14] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:29:02] This is snippy 4.6.0
Show full stderr[00:29:02] This is snippy 4.6.0 [00:29:02] Written by Torsten Seemann [00:29:02] Obtained from https://github.com/tseemann/snippy [00:29:02] Detected operating system: linux [00:29:02] Enabling bundled linux tools. [00:29:03] Found bwa - /usr/local/bin/bwa [00:29:03] Found bcftools - /usr/local/bin/bcftools [00:29:03] Found samtools - /usr/local/bin/samtools [00:29:03] Found java - /usr/local/bin/java [00:29:03] Found snpEff - /usr/local/bin/snpEff [00:29:03] Found samclip - /usr/local/bin/samclip [00:29:03] Found seqtk - /usr/local/bin/seqtk [00:29:03] Found parallel - /usr/local/bin/parallel [00:29:03] Found freebayes - /usr/local/bin/freebayes [00:29:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:29:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:29:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:29:03] Found vcfuniq - /usr/local/bin/vcfuniq [00:29:03] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:29:03] Found gzip - /bin/gzip [00:29:03] Found vt - /usr/local/bin/vt [00:29:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:29:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:29:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:29:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:29:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:29:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:29:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:29:03] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:29:36] This is snippy 4.6.0
Show full stderr[00:29:36] This is snippy 4.6.0 [00:29:36] Written by Torsten Seemann [00:29:36] Obtained from https://github.com/tseemann/snippy [00:29:36] Detected operating system: linux [00:29:36] Enabling bundled linux tools. [00:29:36] Found bwa - /usr/local/bin/bwa [00:29:36] Found bcftools - /usr/local/bin/bcftools [00:29:36] Found samtools - /usr/local/bin/samtools [00:29:36] Found java - /usr/local/bin/java [00:29:36] Found snpEff - /usr/local/bin/snpEff [00:29:36] Found samclip - /usr/local/bin/samclip [00:29:36] Found seqtk - /usr/local/bin/seqtk [00:29:36] Found parallel - /usr/local/bin/parallel [00:29:36] Found freebayes - /usr/local/bin/freebayes [00:29:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:29:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:29:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:29:36] Found vcfuniq - /usr/local/bin/vcfuniq [00:29:36] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:29:36] Found gzip - /bin/gzip [00:29:36] Found vt - /usr/local/bin/vt [00:29:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:29:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:29:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:29:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:29:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:29:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:29:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:29:37] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:29:41] This is snippy 4.6.0
Show full stderr[00:29:41] This is snippy 4.6.0 [00:29:41] Written by Torsten Seemann [00:29:41] Obtained from https://github.com/tseemann/snippy [00:29:41] Detected operating system: linux [00:29:41] Enabling bundled linux tools. [00:29:42] Found bwa - /usr/local/bin/bwa [00:29:42] Found bcftools - /usr/local/bin/bcftools [00:29:42] Found samtools - /usr/local/bin/samtools [00:29:42] Found java - /usr/local/bin/java [00:29:42] Found snpEff - /usr/local/bin/snpEff [00:29:42] Found samclip - /usr/local/bin/samclip [00:29:42] Found seqtk - /usr/local/bin/seqtk [00:29:42] Found parallel - /usr/local/bin/parallel [00:29:42] Found freebayes - /usr/local/bin/freebayes [00:29:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:29:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:29:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:29:42] Found vcfuniq - /usr/local/bin/vcfuniq [00:29:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:29:42] Found gzip - /bin/gzip [00:29:42] Found vt - /usr/local/bin/vt [00:29:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:29:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:29:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:29:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:29:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:29:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:29:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:29:42] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:24:50] This is snippy 4.6.0
Show full stderr[00:24:50] This is snippy 4.6.0 [00:24:50] Written by Torsten Seemann [00:24:50] Obtained from https://github.com/tseemann/snippy [00:24:50] Detected operating system: linux [00:24:50] Enabling bundled linux tools. [00:24:50] Found bwa - /usr/local/bin/bwa [00:24:50] Found bcftools - /usr/local/bin/bcftools [00:24:50] Found samtools - /usr/local/bin/samtools [00:24:50] Found java - /usr/local/bin/java [00:24:50] Found snpEff - /usr/local/bin/snpEff [00:24:50] Found samclip - /usr/local/bin/samclip [00:24:50] Found seqtk - /usr/local/bin/seqtk [00:24:50] Found parallel - /usr/local/bin/parallel [00:24:50] Found freebayes - /usr/local/bin/freebayes [00:24:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:24:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:24:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:24:50] Found vcfuniq - /usr/local/bin/vcfuniq [00:24:50] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:24:50] Found gzip - /bin/gzip [00:24:50] Found vt - /usr/local/bin/vt [00:24:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:24:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:24:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:24:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:24:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:24:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:24:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:24:51] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:26:39] This is snippy 4.6.0
Show full stderr[00:26:39] This is snippy 4.6.0 [00:26:39] Written by Torsten Seemann [00:26:39] Obtained from https://github.com/tseemann/snippy [00:26:39] Detected operating system: linux [00:26:39] Enabling bundled linux tools. [00:26:39] Found bwa - /usr/local/bin/bwa [00:26:39] Found bcftools - /usr/local/bin/bcftools [00:26:39] Found samtools - /usr/local/bin/samtools [00:26:39] Found java - /usr/local/bin/java [00:26:39] Found snpEff - /usr/local/bin/snpEff [00:26:39] Found samclip - /usr/local/bin/samclip [00:26:39] Found seqtk - /usr/local/bin/seqtk [00:26:39] Found parallel - /usr/local/bin/parallel [00:26:39] Found freebayes - /usr/local/bin/freebayes [00:26:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:26:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:26:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:26:39] Found vcfuniq - /usr/local/bin/vcfuniq [00:26:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:26:39] Found gzip - /bin/gzip [00:26:39] Found vt - /usr/local/bin/vt [00:26:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:26:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:26:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:26:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:26:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:26:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:26:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:26:40] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:25:54] This is snippy 4.6.0
Show full stderr[00:25:54] This is snippy 4.6.0 [00:25:54] Written by Torsten Seemann [00:25:54] Obtained from https://github.com/tseemann/snippy [00:25:54] Detected operating system: linux [00:25:54] Enabling bundled linux tools. [00:25:54] Found bwa - /usr/local/bin/bwa [00:25:54] Found bcftools - /usr/local/bin/bcftools [00:25:54] Found samtools - /usr/local/bin/samtools [00:25:54] Found java - /usr/local/bin/java [00:25:54] Found snpEff - /usr/local/bin/snpEff [00:25:54] Found samclip - /usr/local/bin/samclip [00:25:54] Found seqtk - /usr/local/bin/seqtk [00:25:54] Found parallel - /usr/local/bin/parallel [00:25:54] Found freebayes - /usr/local/bin/freebayes [00:25:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:25:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:25:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:25:54] Found vcfuniq - /usr/local/bin/vcfuniq [00:25:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:25:54] Found gzip - /bin/gzip [00:25:54] Found vt - /usr/local/bin/vt [00:25:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:25:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:25:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:25:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:25:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:25:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:25:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:25:55] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:26:01] This is snippy 4.6.0
Show full stderr[00:26:01] This is snippy 4.6.0 [00:26:01] Written by Torsten Seemann [00:26:01] Obtained from https://github.com/tseemann/snippy [00:26:01] Detected operating system: linux [00:26:01] Enabling bundled linux tools. [00:26:01] Found bwa - /usr/local/bin/bwa [00:26:01] Found bcftools - /usr/local/bin/bcftools [00:26:01] Found samtools - /usr/local/bin/samtools [00:26:01] Found java - /usr/local/bin/java [00:26:01] Found snpEff - /usr/local/bin/snpEff [00:26:01] Found samclip - /usr/local/bin/samclip [00:26:01] Found seqtk - /usr/local/bin/seqtk [00:26:01] Found parallel - /usr/local/bin/parallel [00:26:01] Found freebayes - /usr/local/bin/freebayes [00:26:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:26:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:26:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:26:01] Found vcfuniq - /usr/local/bin/vcfuniq [00:26:01] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:26:01] Found gzip - /bin/gzip [00:26:01] Found vt - /usr/local/bin/vt [00:26:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:26:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:26:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:26:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:26:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:26:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:26:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:26:03] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:27:06] This is snippy 4.6.0
Show full stderr[00:27:06] This is snippy 4.6.0 [00:27:06] Written by Torsten Seemann [00:27:06] Obtained from https://github.com/tseemann/snippy [00:27:06] Detected operating system: linux [00:27:06] Enabling bundled linux tools. [00:27:06] Found bwa - /usr/local/bin/bwa [00:27:06] Found bcftools - /usr/local/bin/bcftools [00:27:06] Found samtools - /usr/local/bin/samtools [00:27:06] Found java - /usr/local/bin/java [00:27:06] Found snpEff - /usr/local/bin/snpEff [00:27:06] Found samclip - /usr/local/bin/samclip [00:27:06] Found seqtk - /usr/local/bin/seqtk [00:27:06] Found parallel - /usr/local/bin/parallel [00:27:06] Found freebayes - /usr/local/bin/freebayes [00:27:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:27:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:27:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:27:06] Found vcfuniq - /usr/local/bin/vcfuniq [00:27:06] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:27:06] Found gzip - /bin/gzip [00:27:06] Found vt - /usr/local/bin/vt [00:27:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:27:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:27:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:27:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:27:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:27:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:27:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:27:07] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:29:44] This is snippy 4.6.0
Show full stderr[00:29:44] This is snippy 4.6.0 [00:29:44] Written by Torsten Seemann [00:29:44] Obtained from https://github.com/tseemann/snippy [00:29:44] Detected operating system: linux [00:29:44] Enabling bundled linux tools. [00:29:44] Found bwa - /usr/local/bin/bwa [00:29:44] Found bcftools - /usr/local/bin/bcftools [00:29:44] Found samtools - /usr/local/bin/samtools [00:29:44] Found java - /usr/local/bin/java [00:29:44] Found snpEff - /usr/local/bin/snpEff [00:29:44] Found samclip - /usr/local/bin/samclip [00:29:44] Found seqtk - /usr/local/bin/seqtk [00:29:44] Found parallel - /usr/local/bin/parallel [00:29:44] Found freebayes - /usr/local/bin/freebayes [00:29:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:29:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:29:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:29:44] Found vcfuniq - /usr/local/bin/vcfuniq [00:29:44] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:29:44] Found gzip - /bin/gzip [00:29:44] Found vt - /usr/local/bin/vt [00:29:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:29:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:29:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:29:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:29:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:29:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:29:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:29:45] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:28:53] This is snippy 4.6.0
Show full stderr[00:28:53] This is snippy 4.6.0 [00:28:53] Written by Torsten Seemann [00:28:53] Obtained from https://github.com/tseemann/snippy [00:28:53] Detected operating system: linux [00:28:53] Enabling bundled linux tools. [00:28:53] Found bwa - /usr/local/bin/bwa [00:28:53] Found bcftools - /usr/local/bin/bcftools [00:28:53] Found samtools - /usr/local/bin/samtools [00:28:53] Found java - /usr/local/bin/java [00:28:54] Found snpEff - /usr/local/bin/snpEff [00:28:54] Found samclip - /usr/local/bin/samclip [00:28:54] Found seqtk - /usr/local/bin/seqtk [00:28:54] Found parallel - /usr/local/bin/parallel [00:28:54] Found freebayes - /usr/local/bin/freebayes [00:28:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:28:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:28:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:28:54] Found vcfuniq - /usr/local/bin/vcfuniq [00:28:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:28:54] Found gzip - /bin/gzip [00:28:54] Found vt - /usr/local/bin/vt [00:28:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:28:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:28:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:28:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:28:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:28:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:28:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:28:54] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:29:05] This is snippy 4.6.0
Show full stderr[00:29:05] This is snippy 4.6.0 [00:29:05] Written by Torsten Seemann [00:29:05] Obtained from https://github.com/tseemann/snippy [00:29:05] Detected operating system: linux [00:29:05] Enabling bundled linux tools. [00:29:05] Found bwa - /usr/local/bin/bwa [00:29:05] Found bcftools - /usr/local/bin/bcftools [00:29:05] Found samtools - /usr/local/bin/samtools [00:29:05] Found java - /usr/local/bin/java [00:29:05] Found snpEff - /usr/local/bin/snpEff [00:29:05] Found samclip - /usr/local/bin/samclip [00:29:06] Found seqtk - /usr/local/bin/seqtk [00:29:06] Found parallel - /usr/local/bin/parallel [00:29:06] Found freebayes - /usr/local/bin/freebayes [00:29:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:29:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:29:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:29:06] Found vcfuniq - /usr/local/bin/vcfuniq [00:29:06] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:29:06] Found gzip - /bin/gzip [00:29:06] Found vt - /usr/local/bin/vt [00:29:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:29:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:29:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:29:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:29:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:29:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:29:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:29:06] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:29:12] This is snippy 4.6.0
Show full stderr[00:29:12] This is snippy 4.6.0 [00:29:12] Written by Torsten Seemann [00:29:12] Obtained from https://github.com/tseemann/snippy [00:29:12] Detected operating system: linux [00:29:12] Enabling bundled linux tools. [00:29:12] Found bwa - /usr/local/bin/bwa [00:29:12] Found bcftools - /usr/local/bin/bcftools [00:29:12] Found samtools - /usr/local/bin/samtools [00:29:12] Found java - /usr/local/bin/java [00:29:12] Found snpEff - /usr/local/bin/snpEff [00:29:12] Found samclip - /usr/local/bin/samclip [00:29:12] Found seqtk - /usr/local/bin/seqtk [00:29:12] Found parallel - /usr/local/bin/parallel [00:29:12] Found freebayes - /usr/local/bin/freebayes [00:29:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:29:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:29:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:29:12] Found vcfuniq - /usr/local/bin/vcfuniq [00:29:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:29:12] Found gzip - /bin/gzip [00:29:12] Found vt - /usr/local/bin/vt [00:29:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:29:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:29:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:29:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:29:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:29:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:29:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:29:13] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:27:18] This is snippy 4.6.0
Show full stderr[00:27:18] This is snippy 4.6.0 [00:27:18] Written by Torsten Seemann [00:27:18] Obtained from https://github.com/tseemann/snippy [00:27:18] Detected operating system: linux [00:27:18] Enabling bundled linux tools. [00:27:18] Found bwa - /usr/local/bin/bwa [00:27:18] Found bcftools - /usr/local/bin/bcftools [00:27:18] Found samtools - /usr/local/bin/samtools [00:27:18] Found java - /usr/local/bin/java [00:27:18] Found snpEff - /usr/local/bin/snpEff [00:27:18] Found samclip - /usr/local/bin/samclip [00:27:18] Found seqtk - /usr/local/bin/seqtk [00:27:18] Found parallel - /usr/local/bin/parallel [00:27:19] Found freebayes - /usr/local/bin/freebayes [00:27:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:27:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:27:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:27:19] Found vcfuniq - /usr/local/bin/vcfuniq [00:27:19] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:27:19] Found gzip - /bin/gzip [00:27:19] Found vt - /usr/local/bin/vt [00:27:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:27:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:27:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:27:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:27:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:27:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:27:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:27:20] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:26:57] This is snippy 4.6.0
Show full stderr[00:26:57] This is snippy 4.6.0 [00:26:57] Written by Torsten Seemann [00:26:57] Obtained from https://github.com/tseemann/snippy [00:26:57] Detected operating system: linux [00:26:57] Enabling bundled linux tools. [00:26:57] Found bwa - /usr/local/bin/bwa [00:26:57] Found bcftools - /usr/local/bin/bcftools [00:26:57] Found samtools - /usr/local/bin/samtools [00:26:57] Found java - /usr/local/bin/java [00:26:57] Found snpEff - /usr/local/bin/snpEff [00:26:57] Found samclip - /usr/local/bin/samclip [00:26:57] Found seqtk - /usr/local/bin/seqtk [00:26:57] Found parallel - /usr/local/bin/parallel [00:26:57] Found freebayes - /usr/local/bin/freebayes [00:26:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:26:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:26:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:26:58] Found vcfuniq - /usr/local/bin/vcfuniq [00:26:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:26:58] Found gzip - /bin/gzip [00:26:58] Found vt - /usr/local/bin/vt [00:26:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:26:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:26:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:26:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:26:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:26:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:26:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:26:58] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:28:22] This is snippy 4.6.0
Show full stderr[00:28:22] This is snippy 4.6.0 [00:28:22] Written by Torsten Seemann [00:28:22] Obtained from https://github.com/tseemann/snippy [00:28:22] Detected operating system: linux [00:28:22] Enabling bundled linux tools. [00:28:22] Found bwa - /usr/local/bin/bwa [00:28:22] Found bcftools - /usr/local/bin/bcftools [00:28:22] Found samtools - /usr/local/bin/samtools [00:28:22] Found java - /usr/local/bin/java [00:28:22] Found snpEff - /usr/local/bin/snpEff [00:28:22] Found samclip - /usr/local/bin/samclip [00:28:22] Found seqtk - /usr/local/bin/seqtk [00:28:22] Found parallel - /usr/local/bin/parallel [00:28:22] Found freebayes - /usr/local/bin/freebayes [00:28:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:28:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:28:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:28:22] Found vcfuniq - /usr/local/bin/vcfuniq [00:28:22] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:28:22] Found gzip - /bin/gzip [00:28:22] Found vt - /usr/local/bin/vt [00:28:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:28:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:28:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:28:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:28:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:28:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:28:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:28:23] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:28:24] This is snippy 4.6.0
Show full stderr[00:28:24] This is snippy 4.6.0 [00:28:24] Written by Torsten Seemann [00:28:24] Obtained from https://github.com/tseemann/snippy [00:28:24] Detected operating system: linux [00:28:24] Enabling bundled linux tools. [00:28:24] Found bwa - /usr/local/bin/bwa [00:28:24] Found bcftools - /usr/local/bin/bcftools [00:28:24] Found samtools - /usr/local/bin/samtools [00:28:24] Found java - /usr/local/bin/java [00:28:24] Found snpEff - /usr/local/bin/snpEff [00:28:24] Found samclip - /usr/local/bin/samclip [00:28:24] Found seqtk - /usr/local/bin/seqtk [00:28:24] Found parallel - /usr/local/bin/parallel [00:28:24] Found freebayes - /usr/local/bin/freebayes [00:28:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:28:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:28:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:28:25] Found vcfuniq - /usr/local/bin/vcfuniq [00:28:25] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:28:25] Found gzip - /bin/gzip [00:28:25] Found vt - /usr/local/bin/vt [00:28:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:28:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:28:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:28:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:28:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:28:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:28:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:28:25] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:23:42] This is snippy 4.6.0
Show full stderr[00:23:42] This is snippy 4.6.0 [00:23:42] Written by Torsten Seemann [00:23:42] Obtained from https://github.com/tseemann/snippy [00:23:42] Detected operating system: linux [00:23:42] Enabling bundled linux tools. [00:23:42] Found bwa - /usr/local/bin/bwa [00:23:42] Found bcftools - /usr/local/bin/bcftools [00:23:42] Found samtools - /usr/local/bin/samtools [00:23:42] Found java - /usr/local/bin/java [00:23:42] Found snpEff - /usr/local/bin/snpEff [00:23:42] Found samclip - /usr/local/bin/samclip [00:23:42] Found seqtk - /usr/local/bin/seqtk [00:23:42] Found parallel - /usr/local/bin/parallel [00:23:42] Found freebayes - /usr/local/bin/freebayes [00:23:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:23:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:23:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:23:42] Found vcfuniq - /usr/local/bin/vcfuniq [00:23:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:23:42] Found gzip - /bin/gzip [00:23:42] Found vt - /usr/local/bin/vt [00:23:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:23:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:23:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:23:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:23:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:23:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:23:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:23:43] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:23:44] This is snippy 4.6.0
Show full stderr[00:23:44] This is snippy 4.6.0 [00:23:44] Written by Torsten Seemann [00:23:44] Obtained from https://github.com/tseemann/snippy [00:23:44] Detected operating system: linux [00:23:44] Enabling bundled linux tools. [00:23:44] Found bwa - /usr/local/bin/bwa [00:23:44] Found bcftools - /usr/local/bin/bcftools [00:23:44] Found samtools - /usr/local/bin/samtools [00:23:44] Found java - /usr/local/bin/java [00:23:44] Found snpEff - /usr/local/bin/snpEff [00:23:44] Found samclip - /usr/local/bin/samclip [00:23:44] Found seqtk - /usr/local/bin/seqtk [00:23:44] Found parallel - /usr/local/bin/parallel [00:23:44] Found freebayes - /usr/local/bin/freebayes [00:23:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:23:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:23:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:23:44] Found vcfuniq - /usr/local/bin/vcfuniq [00:23:44] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:23:44] Found gzip - /bin/gzip [00:23:44] Found vt - /usr/local/bin/vt [00:23:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:23:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:23:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:23:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:23:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:23:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:23:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:23:45] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:24:14] This is snippy 4.6.0
Show full stderr[00:24:14] This is snippy 4.6.0 [00:24:14] Written by Torsten Seemann [00:24:14] Obtained from https://github.com/tseemann/snippy [00:24:14] Detected operating system: linux [00:24:14] Enabling bundled linux tools. [00:24:14] Found bwa - /usr/local/bin/bwa [00:24:14] Found bcftools - /usr/local/bin/bcftools [00:24:14] Found samtools - /usr/local/bin/samtools [00:24:14] Found java - /usr/local/bin/java [00:24:14] Found snpEff - /usr/local/bin/snpEff [00:24:14] Found samclip - /usr/local/bin/samclip [00:24:14] Found seqtk - /usr/local/bin/seqtk [00:24:14] Found parallel - /usr/local/bin/parallel [00:24:14] Found freebayes - /usr/local/bin/freebayes [00:24:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:24:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:24:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:24:14] Found vcfuniq - /usr/local/bin/vcfuniq [00:24:14] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:24:14] Found gzip - /bin/gzip [00:24:15] Found vt - /usr/local/bin/vt [00:24:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:24:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:24:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:24:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:24:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:24:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:24:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:24:16] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:29:11] This is snippy 4.6.0
Show full stderr[00:29:11] This is snippy 4.6.0 [00:29:11] Written by Torsten Seemann [00:29:11] Obtained from https://github.com/tseemann/snippy [00:29:11] Detected operating system: linux [00:29:11] Enabling bundled linux tools. [00:29:11] Found bwa - /usr/local/bin/bwa [00:29:12] Found bcftools - /usr/local/bin/bcftools [00:29:12] Found samtools - /usr/local/bin/samtools [00:29:12] Found java - /usr/local/bin/java [00:29:12] Found snpEff - /usr/local/bin/snpEff [00:29:12] Found samclip - /usr/local/bin/samclip [00:29:12] Found seqtk - /usr/local/bin/seqtk [00:29:12] Found parallel - /usr/local/bin/parallel [00:29:12] Found freebayes - /usr/local/bin/freebayes [00:29:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:29:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:29:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:29:12] Found vcfuniq - /usr/local/bin/vcfuniq [00:29:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:29:12] Found gzip - /bin/gzip [00:29:12] Found vt - /usr/local/bin/vt [00:29:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:29:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:29:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:29:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:29:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:29:12] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:29:12] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:29:12] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:27:39] This is snippy 4.6.0
Show full stderr[00:27:39] This is snippy 4.6.0 [00:27:39] Written by Torsten Seemann [00:27:39] Obtained from https://github.com/tseemann/snippy [00:27:39] Detected operating system: linux [00:27:39] Enabling bundled linux tools. [00:27:39] Found bwa - /usr/local/bin/bwa [00:27:39] Found bcftools - /usr/local/bin/bcftools [00:27:39] Found samtools - /usr/local/bin/samtools [00:27:39] Found java - /usr/local/bin/java [00:27:39] Found snpEff - /usr/local/bin/snpEff [00:27:39] Found samclip - /usr/local/bin/samclip [00:27:39] Found seqtk - /usr/local/bin/seqtk [00:27:39] Found parallel - /usr/local/bin/parallel [00:27:39] Found freebayes - /usr/local/bin/freebayes [00:27:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:27:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:27:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:27:39] Found vcfuniq - /usr/local/bin/vcfuniq [00:27:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:27:39] Found gzip - /bin/gzip [00:27:40] Found vt - /usr/local/bin/vt [00:27:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:27:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:27:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:27:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:27:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:27:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:27:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:27:40] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:28:13] This is snippy 4.6.0
Show full stderr[00:28:13] This is snippy 4.6.0 [00:28:13] Written by Torsten Seemann [00:28:13] Obtained from https://github.com/tseemann/snippy [00:28:13] Detected operating system: linux [00:28:13] Enabling bundled linux tools. [00:28:13] Found bwa - /usr/local/bin/bwa [00:28:13] Found bcftools - /usr/local/bin/bcftools [00:28:13] Found samtools - /usr/local/bin/samtools [00:28:13] Found java - /usr/local/bin/java [00:28:13] Found snpEff - /usr/local/bin/snpEff [00:28:13] Found samclip - /usr/local/bin/samclip [00:28:13] Found seqtk - /usr/local/bin/seqtk [00:28:13] Found parallel - /usr/local/bin/parallel [00:28:13] Found freebayes - /usr/local/bin/freebayes [00:28:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:28:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:28:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:28:13] Found vcfuniq - /usr/local/bin/vcfuniq [00:28:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:28:13] Found gzip - /bin/gzip [00:28:13] Found vt - /usr/local/bin/vt [00:28:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:28:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:28:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:28:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:28:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:28:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:28:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:28:14] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:41:15] This is snippy 4.6.0
Show full stderr[00:41:15] This is snippy 4.6.0 [00:41:15] Written by Torsten Seemann [00:41:15] Obtained from https://github.com/tseemann/snippy [00:41:15] Detected operating system: linux [00:41:15] Enabling bundled linux tools. [00:41:15] Found bwa - /usr/local/bin/bwa [00:41:15] Found bcftools - /usr/local/bin/bcftools [00:41:15] Found samtools - /usr/local/bin/samtools [00:41:15] Found java - /usr/local/bin/java [00:41:15] Found snpEff - /usr/local/bin/snpEff [00:41:15] Found samclip - /usr/local/bin/samclip [00:41:15] Found seqtk - /usr/local/bin/seqtk [00:41:15] Found parallel - /usr/local/bin/parallel [00:41:15] Found freebayes - /usr/local/bin/freebayes [00:41:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:41:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:41:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:41:15] Found vcfuniq - /usr/local/bin/vcfuniq [00:41:15] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:41:15] Found gzip - /bin/gzip [00:41:15] Found vt - /usr/local/bin/vt [00:41:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:41:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:41:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:41:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:41:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:41:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:41:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:41:16] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:30:48] This is snippy 4.6.0
Show full stderr[00:30:48] This is snippy 4.6.0 [00:30:48] Written by Torsten Seemann [00:30:48] Obtained from https://github.com/tseemann/snippy [00:30:48] Detected operating system: linux [00:30:48] Enabling bundled linux tools. [00:30:48] Found bwa - /usr/local/bin/bwa [00:30:48] Found bcftools - /usr/local/bin/bcftools [00:30:48] Found samtools - /usr/local/bin/samtools [00:30:48] Found java - /usr/local/bin/java [00:30:48] Found snpEff - /usr/local/bin/snpEff [00:30:48] Found samclip - /usr/local/bin/samclip [00:30:48] Found seqtk - /usr/local/bin/seqtk [00:30:48] Found parallel - /usr/local/bin/parallel [00:30:48] Found freebayes - /usr/local/bin/freebayes [00:30:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:30:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:30:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:30:48] Found vcfuniq - /usr/local/bin/vcfuniq [00:30:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:30:48] Found gzip - /bin/gzip [00:30:48] Found vt - /usr/local/bin/vt [00:30:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:30:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:30:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:30:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:30:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:30:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:30:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:30:49] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:31:21] This is snippy 4.6.0
Show full stderr[00:31:21] This is snippy 4.6.0 [00:31:21] Written by Torsten Seemann [00:31:21] Obtained from https://github.com/tseemann/snippy [00:31:21] Detected operating system: linux [00:31:21] Enabling bundled linux tools. [00:31:21] Found bwa - /usr/local/bin/bwa [00:31:21] Found bcftools - /usr/local/bin/bcftools [00:31:21] Found samtools - /usr/local/bin/samtools [00:31:21] Found java - /usr/local/bin/java [00:31:21] Found snpEff - /usr/local/bin/snpEff [00:31:21] Found samclip - /usr/local/bin/samclip [00:31:21] Found seqtk - /usr/local/bin/seqtk [00:31:21] Found parallel - /usr/local/bin/parallel [00:31:21] Found freebayes - /usr/local/bin/freebayes [00:31:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:31:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:31:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:31:21] Found vcfuniq - /usr/local/bin/vcfuniq [00:31:21] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:31:21] Found gzip - /bin/gzip [00:31:21] Found vt - /usr/local/bin/vt [00:31:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:31:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:31:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:31:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:31:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:31:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:31:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:31:22] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:29:42] This is snippy 4.6.0
Show full stderr[00:29:42] This is snippy 4.6.0 [00:29:42] Written by Torsten Seemann [00:29:42] Obtained from https://github.com/tseemann/snippy [00:29:42] Detected operating system: linux [00:29:42] Enabling bundled linux tools. [00:29:42] Found bwa - /usr/local/bin/bwa [00:29:42] Found bcftools - /usr/local/bin/bcftools [00:29:42] Found samtools - /usr/local/bin/samtools [00:29:42] Found java - /usr/local/bin/java [00:29:42] Found snpEff - /usr/local/bin/snpEff [00:29:42] Found samclip - /usr/local/bin/samclip [00:29:42] Found seqtk - /usr/local/bin/seqtk [00:29:42] Found parallel - /usr/local/bin/parallel [00:29:42] Found freebayes - /usr/local/bin/freebayes [00:29:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:29:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:29:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:29:42] Found vcfuniq - /usr/local/bin/vcfuniq [00:29:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:29:42] Found gzip - /bin/gzip [00:29:42] Found vt - /usr/local/bin/vt [00:29:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:29:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:29:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:29:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:29:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:29:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:29:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:29:42] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:30:57] This is snippy 4.6.0
Show full stderr[00:30:57] This is snippy 4.6.0 [00:30:57] Written by Torsten Seemann [00:30:57] Obtained from https://github.com/tseemann/snippy [00:30:57] Detected operating system: linux [00:30:57] Enabling bundled linux tools. [00:30:57] Found bwa - /usr/local/bin/bwa [00:30:57] Found bcftools - /usr/local/bin/bcftools [00:30:57] Found samtools - /usr/local/bin/samtools [00:30:57] Found java - /usr/local/bin/java [00:30:57] Found snpEff - /usr/local/bin/snpEff [00:30:57] Found samclip - /usr/local/bin/samclip [00:30:57] Found seqtk - /usr/local/bin/seqtk [00:30:57] Found parallel - /usr/local/bin/parallel [00:30:57] Found freebayes - /usr/local/bin/freebayes [00:30:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:30:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:30:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:30:57] Found vcfuniq - /usr/local/bin/vcfuniq [00:30:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:30:57] Found gzip - /bin/gzip [00:30:57] Found vt - /usr/local/bin/vt [00:30:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:30:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:30:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:30:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:30:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:30:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:30:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:30:58] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:31:39] This is snippy 4.6.0
Show full stderr[00:31:39] This is snippy 4.6.0 [00:31:39] Written by Torsten Seemann [00:31:39] Obtained from https://github.com/tseemann/snippy [00:31:39] Detected operating system: linux [00:31:39] Enabling bundled linux tools. [00:31:39] Found bwa - /usr/local/bin/bwa [00:31:39] Found bcftools - /usr/local/bin/bcftools [00:31:39] Found samtools - /usr/local/bin/samtools [00:31:39] Found java - /usr/local/bin/java [00:31:39] Found snpEff - /usr/local/bin/snpEff [00:31:39] Found samclip - /usr/local/bin/samclip [00:31:39] Found seqtk - /usr/local/bin/seqtk [00:31:39] Found parallel - /usr/local/bin/parallel [00:31:39] Found freebayes - /usr/local/bin/freebayes [00:31:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:31:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:31:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:31:39] Found vcfuniq - /usr/local/bin/vcfuniq [00:31:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:31:39] Found gzip - /bin/gzip [00:31:39] Found vt - /usr/local/bin/vt [00:31:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:31:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:31:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:31:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:31:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:31:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:31:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:31:40] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:32:54] This is snippy 4.6.0
Show full stderr[00:32:54] This is snippy 4.6.0 [00:32:54] Written by Torsten Seemann [00:32:54] Obtained from https://github.com/tseemann/snippy [00:32:54] Detected operating system: linux [00:32:54] Enabling bundled linux tools. [00:32:54] Found bwa - /usr/local/bin/bwa [00:32:54] Found bcftools - /usr/local/bin/bcftools [00:32:54] Found samtools - /usr/local/bin/samtools [00:32:54] Found java - /usr/local/bin/java [00:32:54] Found snpEff - /usr/local/bin/snpEff [00:32:54] Found samclip - /usr/local/bin/samclip [00:32:54] Found seqtk - /usr/local/bin/seqtk [00:32:54] Found parallel - /usr/local/bin/parallel [00:32:54] Found freebayes - /usr/local/bin/freebayes [00:32:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:32:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:32:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:32:54] Found vcfuniq - /usr/local/bin/vcfuniq [00:32:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:32:54] Found gzip - /bin/gzip [00:32:54] Found vt - /usr/local/bin/vt [00:32:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:32:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:32:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:32:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:32:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:32:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:32:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:32:55] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:48:05] This is snippy 4.6.0
Show full stderr[00:48:05] This is snippy 4.6.0 [00:48:05] Written by Torsten Seemann [00:48:05] Obtained from https://github.com/tseemann/snippy [00:48:05] Detected operating system: linux [00:48:05] Enabling bundled linux tools. [00:48:05] Found bwa - /usr/local/bin/bwa [00:48:05] Found bcftools - /usr/local/bin/bcftools [00:48:05] Found samtools - /usr/local/bin/samtools [00:48:05] Found java - /usr/local/bin/java [00:48:05] Found snpEff - /usr/local/bin/snpEff [00:48:05] Found samclip - /usr/local/bin/samclip [00:48:05] Found seqtk - /usr/local/bin/seqtk [00:48:05] Found parallel - /usr/local/bin/parallel [00:48:05] Found freebayes - /usr/local/bin/freebayes [00:48:05] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:48:05] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:48:05] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:48:05] Found vcfuniq - /usr/local/bin/vcfuniq [00:48:05] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:48:05] Found gzip - /bin/gzip [00:48:05] Found vt - /usr/local/bin/vt [00:48:05] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:48:05] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:48:05] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:48:05] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:48:05] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:48:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:48:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:48:06] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:06:25] This is snippy 4.6.0
Show full stderr[01:06:25] This is snippy 4.6.0 [01:06:25] Written by Torsten Seemann [01:06:25] Obtained from https://github.com/tseemann/snippy [01:06:25] Detected operating system: linux [01:06:25] Enabling bundled linux tools. [01:06:25] Found bwa - /usr/local/bin/bwa [01:06:25] Found bcftools - /usr/local/bin/bcftools [01:06:25] Found samtools - /usr/local/bin/samtools [01:06:25] Found java - /usr/local/bin/java [01:06:25] Found snpEff - /usr/local/bin/snpEff [01:06:25] Found samclip - /usr/local/bin/samclip [01:06:25] Found seqtk - /usr/local/bin/seqtk [01:06:25] Found parallel - /usr/local/bin/parallel [01:06:25] Found freebayes - /usr/local/bin/freebayes [01:06:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:06:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:06:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:06:25] Found vcfuniq - /usr/local/bin/vcfuniq [01:06:25] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:06:25] Found gzip - /bin/gzip [01:06:25] Found vt - /usr/local/bin/vt [01:06:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:06:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:06:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:06:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:06:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:06:26] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:06:26] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:06:26] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:34:48] This is snippy 4.6.0
Show full stderr[00:34:48] This is snippy 4.6.0 [00:34:48] Written by Torsten Seemann [00:34:48] Obtained from https://github.com/tseemann/snippy [00:34:48] Detected operating system: linux [00:34:48] Enabling bundled linux tools. [00:34:48] Found bwa - /usr/local/bin/bwa [00:34:48] Found bcftools - /usr/local/bin/bcftools [00:34:48] Found samtools - /usr/local/bin/samtools [00:34:48] Found java - /usr/local/bin/java [00:34:48] Found snpEff - /usr/local/bin/snpEff [00:34:48] Found samclip - /usr/local/bin/samclip [00:34:48] Found seqtk - /usr/local/bin/seqtk [00:34:48] Found parallel - /usr/local/bin/parallel [00:34:48] Found freebayes - /usr/local/bin/freebayes [00:34:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:34:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:34:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:34:48] Found vcfuniq - /usr/local/bin/vcfuniq [00:34:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:34:48] Found gzip - /bin/gzip [00:34:48] Found vt - /usr/local/bin/vt [00:34:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:34:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:34:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:34:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:34:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:34:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:34:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:34:49] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:35:24] This is snippy 4.6.0
Show full stderr[00:35:24] This is snippy 4.6.0 [00:35:24] Written by Torsten Seemann [00:35:24] Obtained from https://github.com/tseemann/snippy [00:35:24] Detected operating system: linux [00:35:24] Enabling bundled linux tools. [00:35:24] Found bwa - /usr/local/bin/bwa [00:35:24] Found bcftools - /usr/local/bin/bcftools [00:35:24] Found samtools - /usr/local/bin/samtools [00:35:24] Found java - /usr/local/bin/java [00:35:24] Found snpEff - /usr/local/bin/snpEff [00:35:24] Found samclip - /usr/local/bin/samclip [00:35:24] Found seqtk - /usr/local/bin/seqtk [00:35:24] Found parallel - /usr/local/bin/parallel [00:35:24] Found freebayes - /usr/local/bin/freebayes [00:35:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:35:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:35:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:35:24] Found vcfuniq - /usr/local/bin/vcfuniq [00:35:24] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:35:24] Found gzip - /bin/gzip [00:35:24] Found vt - /usr/local/bin/vt [00:35:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:35:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:35:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:35:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:35:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:35:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:35:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:35:25] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:44:57] This is snippy 4.6.0
Show full stderr[00:44:57] This is snippy 4.6.0 [00:44:57] Written by Torsten Seemann [00:44:57] Obtained from https://github.com/tseemann/snippy [00:44:57] Detected operating system: linux [00:44:57] Enabling bundled linux tools. [00:44:57] Found bwa - /usr/local/bin/bwa [00:44:57] Found bcftools - /usr/local/bin/bcftools [00:44:57] Found samtools - /usr/local/bin/samtools [00:44:57] Found java - /usr/local/bin/java [00:44:57] Found snpEff - /usr/local/bin/snpEff [00:44:57] Found samclip - /usr/local/bin/samclip [00:44:57] Found seqtk - /usr/local/bin/seqtk [00:44:57] Found parallel - /usr/local/bin/parallel [00:44:57] Found freebayes - /usr/local/bin/freebayes [00:44:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:44:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:44:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:44:57] Found vcfuniq - /usr/local/bin/vcfuniq [00:44:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:44:57] Found gzip - /bin/gzip [00:44:57] Found vt - /usr/local/bin/vt [00:44:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:44:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:44:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:44:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:44:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:44:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:44:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:44:58] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:47:37] This is snippy 4.6.0
Show full stderr[00:47:37] This is snippy 4.6.0 [00:47:37] Written by Torsten Seemann [00:47:37] Obtained from https://github.com/tseemann/snippy [00:47:37] Detected operating system: linux [00:47:37] Enabling bundled linux tools. [00:47:37] Found bwa - /usr/local/bin/bwa [00:47:37] Found bcftools - /usr/local/bin/bcftools [00:47:37] Found samtools - /usr/local/bin/samtools [00:47:37] Found java - /usr/local/bin/java [00:47:37] Found snpEff - /usr/local/bin/snpEff [00:47:37] Found samclip - /usr/local/bin/samclip [00:47:37] Found seqtk - /usr/local/bin/seqtk [00:47:37] Found parallel - /usr/local/bin/parallel [00:47:37] Found freebayes - /usr/local/bin/freebayes [00:47:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:47:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:47:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:47:37] Found vcfuniq - /usr/local/bin/vcfuniq [00:47:37] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:47:37] Found gzip - /bin/gzip [00:47:37] Found vt - /usr/local/bin/vt [00:47:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:47:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:47:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:47:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:47:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:47:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:47:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:47:42] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:51:55] This is snippy 4.6.0
Show full stderr[00:51:55] This is snippy 4.6.0 [00:51:55] Written by Torsten Seemann [00:51:55] Obtained from https://github.com/tseemann/snippy [00:51:55] Detected operating system: linux [00:51:55] Enabling bundled linux tools. [00:51:55] Found bwa - /usr/local/bin/bwa [00:51:55] Found bcftools - /usr/local/bin/bcftools [00:51:55] Found samtools - /usr/local/bin/samtools [00:51:55] Found java - /usr/local/bin/java [00:51:55] Found snpEff - /usr/local/bin/snpEff [00:51:55] Found samclip - /usr/local/bin/samclip [00:51:55] Found seqtk - /usr/local/bin/seqtk [00:51:55] Found parallel - /usr/local/bin/parallel [00:51:55] Found freebayes - /usr/local/bin/freebayes [00:51:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:51:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:51:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:51:55] Found vcfuniq - /usr/local/bin/vcfuniq [00:51:55] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:51:55] Found gzip - /bin/gzip [00:51:55] Found vt - /usr/local/bin/vt [00:51:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:51:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:51:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:51:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:51:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:51:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:51:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:51:56] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:06:54] This is snippy 4.6.0
Show full stderr[01:06:54] This is snippy 4.6.0 [01:06:54] Written by Torsten Seemann [01:06:54] Obtained from https://github.com/tseemann/snippy [01:06:54] Detected operating system: linux [01:06:54] Enabling bundled linux tools. [01:06:54] Found bwa - /usr/local/bin/bwa [01:06:54] Found bcftools - /usr/local/bin/bcftools [01:06:54] Found samtools - /usr/local/bin/samtools [01:06:54] Found java - /usr/local/bin/java [01:06:54] Found snpEff - /usr/local/bin/snpEff [01:06:54] Found samclip - /usr/local/bin/samclip [01:06:54] Found seqtk - /usr/local/bin/seqtk [01:06:54] Found parallel - /usr/local/bin/parallel [01:06:54] Found freebayes - /usr/local/bin/freebayes [01:06:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:06:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:06:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:06:54] Found vcfuniq - /usr/local/bin/vcfuniq [01:06:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:06:54] Found gzip - /bin/gzip [01:06:54] Found vt - /usr/local/bin/vt [01:06:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:06:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:06:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:06:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:06:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:06:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:06:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:06:55] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:59:31] This is snippy 4.6.0
Show full stderr[00:59:31] This is snippy 4.6.0 [00:59:31] Written by Torsten Seemann [00:59:31] Obtained from https://github.com/tseemann/snippy [00:59:31] Detected operating system: linux [00:59:31] Enabling bundled linux tools. [00:59:31] Found bwa - /usr/local/bin/bwa [00:59:31] Found bcftools - /usr/local/bin/bcftools [00:59:31] Found samtools - /usr/local/bin/samtools [00:59:31] Found java - /usr/local/bin/java [00:59:31] Found snpEff - /usr/local/bin/snpEff [00:59:31] Found samclip - /usr/local/bin/samclip [00:59:31] Found seqtk - /usr/local/bin/seqtk [00:59:31] Found parallel - /usr/local/bin/parallel [00:59:31] Found freebayes - /usr/local/bin/freebayes [00:59:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:59:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:59:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:59:31] Found vcfuniq - /usr/local/bin/vcfuniq [00:59:31] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:59:31] Found gzip - /bin/gzip [00:59:31] Found vt - /usr/local/bin/vt [00:59:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:59:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:59:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:59:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:59:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:59:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:59:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:59:32] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:30:14] This is snippy 4.6.0
Show full stderr[00:30:14] This is snippy 4.6.0 [00:30:14] Written by Torsten Seemann [00:30:14] Obtained from https://github.com/tseemann/snippy [00:30:14] Detected operating system: linux [00:30:14] Enabling bundled linux tools. [00:30:14] Found bwa - /usr/local/bin/bwa [00:30:14] Found bcftools - /usr/local/bin/bcftools [00:30:14] Found samtools - /usr/local/bin/samtools [00:30:14] Found java - /usr/local/bin/java [00:30:14] Found snpEff - /usr/local/bin/snpEff [00:30:14] Found samclip - /usr/local/bin/samclip [00:30:14] Found seqtk - /usr/local/bin/seqtk [00:30:14] Found parallel - /usr/local/bin/parallel [00:30:14] Found freebayes - /usr/local/bin/freebayes [00:30:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:30:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:30:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:30:14] Found vcfuniq - /usr/local/bin/vcfuniq [00:30:14] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:30:14] Found gzip - /bin/gzip [00:30:14] Found vt - /usr/local/bin/vt [00:30:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:30:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:30:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:30:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:30:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:30:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:30:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:30:15] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:30:33] This is snippy 4.6.0
Show full stderr[00:30:33] This is snippy 4.6.0 [00:30:33] Written by Torsten Seemann [00:30:33] Obtained from https://github.com/tseemann/snippy [00:30:33] Detected operating system: linux [00:30:33] Enabling bundled linux tools. [00:30:33] Found bwa - /usr/local/bin/bwa [00:30:33] Found bcftools - /usr/local/bin/bcftools [00:30:33] Found samtools - /usr/local/bin/samtools [00:30:33] Found java - /usr/local/bin/java [00:30:33] Found snpEff - /usr/local/bin/snpEff [00:30:33] Found samclip - /usr/local/bin/samclip [00:30:33] Found seqtk - /usr/local/bin/seqtk [00:30:33] Found parallel - /usr/local/bin/parallel [00:30:33] Found freebayes - /usr/local/bin/freebayes [00:30:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:30:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:30:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:30:33] Found vcfuniq - /usr/local/bin/vcfuniq [00:30:33] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:30:33] Found gzip - /bin/gzip [00:30:33] Found vt - /usr/local/bin/vt [00:30:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:30:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:30:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:30:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:30:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:30:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:30:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:30:34] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:31:14] This is snippy 4.6.0
Show full stderr[00:31:14] This is snippy 4.6.0 [00:31:14] Written by Torsten Seemann [00:31:14] Obtained from https://github.com/tseemann/snippy [00:31:14] Detected operating system: linux [00:31:14] Enabling bundled linux tools. [00:31:14] Found bwa - /usr/local/bin/bwa [00:31:14] Found bcftools - /usr/local/bin/bcftools [00:31:14] Found samtools - /usr/local/bin/samtools [00:31:14] Found java - /usr/local/bin/java [00:31:14] Found snpEff - /usr/local/bin/snpEff [00:31:14] Found samclip - /usr/local/bin/samclip [00:31:14] Found seqtk - /usr/local/bin/seqtk [00:31:14] Found parallel - /usr/local/bin/parallel [00:31:14] Found freebayes - /usr/local/bin/freebayes [00:31:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:31:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:31:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:31:14] Found vcfuniq - /usr/local/bin/vcfuniq [00:31:14] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:31:14] Found gzip - /bin/gzip [00:31:14] Found vt - /usr/local/bin/vt [00:31:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:31:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:31:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:31:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:31:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:31:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:31:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:31:15] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:31:15] This is snippy 4.6.0
Show full stderr[00:31:15] This is snippy 4.6.0 [00:31:15] Written by Torsten Seemann [00:31:15] Obtained from https://github.com/tseemann/snippy [00:31:15] Detected operating system: linux [00:31:15] Enabling bundled linux tools. [00:31:15] Found bwa - /usr/local/bin/bwa [00:31:15] Found bcftools - /usr/local/bin/bcftools [00:31:15] Found samtools - /usr/local/bin/samtools [00:31:15] Found java - /usr/local/bin/java [00:31:15] Found snpEff - /usr/local/bin/snpEff [00:31:15] Found samclip - /usr/local/bin/samclip [00:31:15] Found seqtk - /usr/local/bin/seqtk [00:31:15] Found parallel - /usr/local/bin/parallel [00:31:15] Found freebayes - /usr/local/bin/freebayes [00:31:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:31:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:31:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:31:15] Found vcfuniq - /usr/local/bin/vcfuniq [00:31:15] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:31:15] Found gzip - /bin/gzip [00:31:15] Found vt - /usr/local/bin/vt [00:31:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:31:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:31:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:31:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:31:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:31:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:31:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:31:16] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:31:24] This is snippy 4.6.0
Show full stderr[00:31:24] This is snippy 4.6.0 [00:31:24] Written by Torsten Seemann [00:31:24] Obtained from https://github.com/tseemann/snippy [00:31:24] Detected operating system: linux [00:31:24] Enabling bundled linux tools. [00:31:24] Found bwa - /usr/local/bin/bwa [00:31:24] Found bcftools - /usr/local/bin/bcftools [00:31:24] Found samtools - /usr/local/bin/samtools [00:31:24] Found java - /usr/local/bin/java [00:31:24] Found snpEff - /usr/local/bin/snpEff [00:31:24] Found samclip - /usr/local/bin/samclip [00:31:24] Found seqtk - /usr/local/bin/seqtk [00:31:24] Found parallel - /usr/local/bin/parallel [00:31:24] Found freebayes - /usr/local/bin/freebayes [00:31:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:31:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:31:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:31:24] Found vcfuniq - /usr/local/bin/vcfuniq [00:31:24] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:31:24] Found gzip - /bin/gzip [00:31:24] Found vt - /usr/local/bin/vt [00:31:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:31:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:31:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:31:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:31:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:31:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:31:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:31:25] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:33:00] This is snippy 4.6.0
Show full stderr[00:33:00] This is snippy 4.6.0 [00:33:00] Written by Torsten Seemann [00:33:00] Obtained from https://github.com/tseemann/snippy [00:33:00] Detected operating system: linux [00:33:00] Enabling bundled linux tools. [00:33:00] Found bwa - /usr/local/bin/bwa [00:33:00] Found bcftools - /usr/local/bin/bcftools [00:33:00] Found samtools - /usr/local/bin/samtools [00:33:00] Found java - /usr/local/bin/java [00:33:00] Found snpEff - /usr/local/bin/snpEff [00:33:00] Found samclip - /usr/local/bin/samclip [00:33:00] Found seqtk - /usr/local/bin/seqtk [00:33:00] Found parallel - /usr/local/bin/parallel [00:33:00] Found freebayes - /usr/local/bin/freebayes [00:33:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:33:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:33:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:33:00] Found vcfuniq - /usr/local/bin/vcfuniq [00:33:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:33:00] Found gzip - /bin/gzip [00:33:00] Found vt - /usr/local/bin/vt [00:33:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:33:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:33:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:33:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:33:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:33:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:33:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:33:01] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:58:36] This is snippy 4.6.0
Show full stderr[00:58:36] This is snippy 4.6.0 [00:58:36] Written by Torsten Seemann [00:58:36] Obtained from https://github.com/tseemann/snippy [00:58:36] Detected operating system: linux [00:58:36] Enabling bundled linux tools. [00:58:36] Found bwa - /usr/local/bin/bwa [00:58:36] Found bcftools - /usr/local/bin/bcftools [00:58:36] Found samtools - /usr/local/bin/samtools [00:58:36] Found java - /usr/local/bin/java [00:58:36] Found snpEff - /usr/local/bin/snpEff [00:58:36] Found samclip - /usr/local/bin/samclip [00:58:36] Found seqtk - /usr/local/bin/seqtk [00:58:36] Found parallel - /usr/local/bin/parallel [00:58:36] Found freebayes - /usr/local/bin/freebayes [00:58:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:58:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:58:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:58:36] Found vcfuniq - /usr/local/bin/vcfuniq [00:58:36] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:58:36] Found gzip - /bin/gzip [00:58:36] Found vt - /usr/local/bin/vt [00:58:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:58:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:58:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:58:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:58:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:58:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:58:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:58:37] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:26:04] This is snippy 4.6.0
Show full stderr[00:26:04] This is snippy 4.6.0 [00:26:04] Written by Torsten Seemann [00:26:04] Obtained from https://github.com/tseemann/snippy [00:26:04] Detected operating system: linux [00:26:04] Enabling bundled linux tools. [00:26:04] Found bwa - /usr/local/bin/bwa [00:26:04] Found bcftools - /usr/local/bin/bcftools [00:26:04] Found samtools - /usr/local/bin/samtools [00:26:04] Found java - /usr/local/bin/java [00:26:04] Found snpEff - /usr/local/bin/snpEff [00:26:04] Found samclip - /usr/local/bin/samclip [00:26:04] Found seqtk - /usr/local/bin/seqtk [00:26:04] Found parallel - /usr/local/bin/parallel [00:26:04] Found freebayes - /usr/local/bin/freebayes [00:26:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:26:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:26:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:26:04] Found vcfuniq - /usr/local/bin/vcfuniq [00:26:04] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:26:04] Found gzip - /bin/gzip [00:26:04] Found vt - /usr/local/bin/vt [00:26:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:26:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:26:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:26:05] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:26:05] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:26:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:26:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:26:06] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:26:06] This is snippy 4.6.0
Show full stderr[00:26:06] This is snippy 4.6.0 [00:26:06] Written by Torsten Seemann [00:26:06] Obtained from https://github.com/tseemann/snippy [00:26:06] Detected operating system: linux [00:26:06] Enabling bundled linux tools. [00:26:06] Found bwa - /usr/local/bin/bwa [00:26:06] Found bcftools - /usr/local/bin/bcftools [00:26:06] Found samtools - /usr/local/bin/samtools [00:26:06] Found java - /usr/local/bin/java [00:26:06] Found snpEff - /usr/local/bin/snpEff [00:26:06] Found samclip - /usr/local/bin/samclip [00:26:06] Found seqtk - /usr/local/bin/seqtk [00:26:06] Found parallel - /usr/local/bin/parallel [00:26:06] Found freebayes - /usr/local/bin/freebayes [00:26:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:26:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:26:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:26:06] Found vcfuniq - /usr/local/bin/vcfuniq [00:26:06] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:26:06] Found gzip - /bin/gzip [00:26:06] Found vt - /usr/local/bin/vt [00:26:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:26:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:26:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:26:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:26:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:26:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:26:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:26:07] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:26:24] This is snippy 4.6.0
Show full stderr[00:26:24] This is snippy 4.6.0 [00:26:24] Written by Torsten Seemann [00:26:24] Obtained from https://github.com/tseemann/snippy [00:26:24] Detected operating system: linux [00:26:24] Enabling bundled linux tools. [00:26:24] Found bwa - /usr/local/bin/bwa [00:26:24] Found bcftools - /usr/local/bin/bcftools [00:26:24] Found samtools - /usr/local/bin/samtools [00:26:24] Found java - /usr/local/bin/java [00:26:24] Found snpEff - /usr/local/bin/snpEff [00:26:24] Found samclip - /usr/local/bin/samclip [00:26:24] Found seqtk - /usr/local/bin/seqtk [00:26:24] Found parallel - /usr/local/bin/parallel [00:26:24] Found freebayes - /usr/local/bin/freebayes [00:26:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:26:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:26:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:26:24] Found vcfuniq - /usr/local/bin/vcfuniq [00:26:24] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:26:24] Found gzip - /bin/gzip [00:26:24] Found vt - /usr/local/bin/vt [00:26:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:26:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:26:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:26:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:26:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:26:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:26:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:26:25] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:27:42] This is snippy 4.6.0
Show full stderr[00:27:42] This is snippy 4.6.0 [00:27:42] Written by Torsten Seemann [00:27:42] Obtained from https://github.com/tseemann/snippy [00:27:42] Detected operating system: linux [00:27:42] Enabling bundled linux tools. [00:27:42] Found bwa - /usr/local/bin/bwa [00:27:42] Found bcftools - /usr/local/bin/bcftools [00:27:42] Found samtools - /usr/local/bin/samtools [00:27:43] Found java - /usr/local/bin/java [00:27:43] Found snpEff - /usr/local/bin/snpEff [00:27:43] Found samclip - /usr/local/bin/samclip [00:27:43] Found seqtk - /usr/local/bin/seqtk [00:27:43] Found parallel - /usr/local/bin/parallel [00:27:43] Found freebayes - /usr/local/bin/freebayes [00:27:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:27:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:27:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:27:43] Found vcfuniq - /usr/local/bin/vcfuniq [00:27:43] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:27:43] Found gzip - /bin/gzip [00:27:43] Found vt - /usr/local/bin/vt [00:27:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:27:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:27:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:27:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:27:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:27:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:27:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:27:44] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:27:58] This is snippy 4.6.0
Show full stderr[00:27:58] This is snippy 4.6.0 [00:27:58] Written by Torsten Seemann [00:27:58] Obtained from https://github.com/tseemann/snippy [00:27:58] Detected operating system: linux [00:27:58] Enabling bundled linux tools. [00:27:58] Found bwa - /usr/local/bin/bwa [00:27:58] Found bcftools - /usr/local/bin/bcftools [00:27:58] Found samtools - /usr/local/bin/samtools [00:27:58] Found java - /usr/local/bin/java [00:27:58] Found snpEff - /usr/local/bin/snpEff [00:27:58] Found samclip - /usr/local/bin/samclip [00:27:58] Found seqtk - /usr/local/bin/seqtk [00:27:58] Found parallel - /usr/local/bin/parallel [00:27:58] Found freebayes - /usr/local/bin/freebayes [00:27:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:27:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:27:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:27:58] Found vcfuniq - /usr/local/bin/vcfuniq [00:27:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:27:58] Found gzip - /bin/gzip [00:27:58] Found vt - /usr/local/bin/vt [00:27:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:27:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:27:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:27:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:27:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:27:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:27:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:27:59] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:28:33] This is snippy 4.6.0
Show full stderr[00:28:33] This is snippy 4.6.0 [00:28:33] Written by Torsten Seemann [00:28:33] Obtained from https://github.com/tseemann/snippy [00:28:33] Detected operating system: linux [00:28:33] Enabling bundled linux tools. [00:28:33] Found bwa - /usr/local/bin/bwa [00:28:33] Found bcftools - /usr/local/bin/bcftools [00:28:33] Found samtools - /usr/local/bin/samtools [00:28:33] Found java - /usr/local/bin/java [00:28:33] Found snpEff - /usr/local/bin/snpEff [00:28:33] Found samclip - /usr/local/bin/samclip [00:28:33] Found seqtk - /usr/local/bin/seqtk [00:28:33] Found parallel - /usr/local/bin/parallel [00:28:33] Found freebayes - /usr/local/bin/freebayes [00:28:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:28:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:28:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:28:34] Found vcfuniq - /usr/local/bin/vcfuniq [00:28:34] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:28:34] Found gzip - /bin/gzip [00:28:34] Found vt - /usr/local/bin/vt [00:28:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:28:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:28:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:28:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:28:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:28:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:28:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:28:34] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:28:50] This is snippy 4.6.0
Show full stderr[00:28:50] This is snippy 4.6.0 [00:28:50] Written by Torsten Seemann [00:28:50] Obtained from https://github.com/tseemann/snippy [00:28:50] Detected operating system: linux [00:28:50] Enabling bundled linux tools. [00:28:50] Found bwa - /usr/local/bin/bwa [00:28:50] Found bcftools - /usr/local/bin/bcftools [00:28:50] Found samtools - /usr/local/bin/samtools [00:28:50] Found java - /usr/local/bin/java [00:28:50] Found snpEff - /usr/local/bin/snpEff [00:28:50] Found samclip - /usr/local/bin/samclip [00:28:50] Found seqtk - /usr/local/bin/seqtk [00:28:50] Found parallel - /usr/local/bin/parallel [00:28:50] Found freebayes - /usr/local/bin/freebayes [00:28:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:28:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:28:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:28:51] Found vcfuniq - /usr/local/bin/vcfuniq [00:28:51] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:28:51] Found gzip - /bin/gzip [00:28:51] Found vt - /usr/local/bin/vt [00:28:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:28:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:28:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:28:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:28:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:28:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:28:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:28:51] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:28:54] This is snippy 4.6.0
Show full stderr[00:28:54] This is snippy 4.6.0 [00:28:54] Written by Torsten Seemann [00:28:54] Obtained from https://github.com/tseemann/snippy [00:28:54] Detected operating system: linux [00:28:54] Enabling bundled linux tools. [00:28:54] Found bwa - /usr/local/bin/bwa [00:28:54] Found bcftools - /usr/local/bin/bcftools [00:28:54] Found samtools - /usr/local/bin/samtools [00:28:54] Found java - /usr/local/bin/java [00:28:54] Found snpEff - /usr/local/bin/snpEff [00:28:54] Found samclip - /usr/local/bin/samclip [00:28:54] Found seqtk - /usr/local/bin/seqtk [00:28:54] Found parallel - /usr/local/bin/parallel [00:28:54] Found freebayes - /usr/local/bin/freebayes [00:28:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:28:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:28:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:28:54] Found vcfuniq - /usr/local/bin/vcfuniq [00:28:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:28:54] Found gzip - /bin/gzip [00:28:54] Found vt - /usr/local/bin/vt [00:28:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:28:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:28:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:28:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:28:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:28:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:28:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:28:55] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:28:57] This is snippy 4.6.0
Show full stderr[00:28:57] This is snippy 4.6.0 [00:28:57] Written by Torsten Seemann [00:28:57] Obtained from https://github.com/tseemann/snippy [00:28:57] Detected operating system: linux [00:28:57] Enabling bundled linux tools. [00:28:57] Found bwa - /usr/local/bin/bwa [00:28:57] Found bcftools - /usr/local/bin/bcftools [00:28:57] Found samtools - /usr/local/bin/samtools [00:28:57] Found java - /usr/local/bin/java [00:28:57] Found snpEff - /usr/local/bin/snpEff [00:28:57] Found samclip - /usr/local/bin/samclip [00:28:57] Found seqtk - /usr/local/bin/seqtk [00:28:57] Found parallel - /usr/local/bin/parallel [00:28:57] Found freebayes - /usr/local/bin/freebayes [00:28:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:28:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:28:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:28:57] Found vcfuniq - /usr/local/bin/vcfuniq [00:28:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:28:57] Found gzip - /bin/gzip [00:28:57] Found vt - /usr/local/bin/vt [00:28:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:28:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:28:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:28:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:28:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:28:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:28:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:28:57] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:29:18] This is snippy 4.6.0
Show full stderr[00:29:18] This is snippy 4.6.0 [00:29:18] Written by Torsten Seemann [00:29:18] Obtained from https://github.com/tseemann/snippy [00:29:18] Detected operating system: linux [00:29:18] Enabling bundled linux tools. [00:29:18] Found bwa - /usr/local/bin/bwa [00:29:18] Found bcftools - /usr/local/bin/bcftools [00:29:18] Found samtools - /usr/local/bin/samtools [00:29:18] Found java - /usr/local/bin/java [00:29:18] Found snpEff - /usr/local/bin/snpEff [00:29:18] Found samclip - /usr/local/bin/samclip [00:29:18] Found seqtk - /usr/local/bin/seqtk [00:29:18] Found parallel - /usr/local/bin/parallel [00:29:18] Found freebayes - /usr/local/bin/freebayes [00:29:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:29:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:29:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:29:18] Found vcfuniq - /usr/local/bin/vcfuniq [00:29:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:29:18] Found gzip - /bin/gzip [00:29:18] Found vt - /usr/local/bin/vt [00:29:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:29:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:29:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:29:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:29:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:29:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:29:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:29:19] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:29:21] This is snippy 4.6.0
Show full stderr[00:29:21] This is snippy 4.6.0 [00:29:21] Written by Torsten Seemann [00:29:21] Obtained from https://github.com/tseemann/snippy [00:29:21] Detected operating system: linux [00:29:21] Enabling bundled linux tools. [00:29:21] Found bwa - /usr/local/bin/bwa [00:29:21] Found bcftools - /usr/local/bin/bcftools [00:29:21] Found samtools - /usr/local/bin/samtools [00:29:21] Found java - /usr/local/bin/java [00:29:21] Found snpEff - /usr/local/bin/snpEff [00:29:21] Found samclip - /usr/local/bin/samclip [00:29:21] Found seqtk - /usr/local/bin/seqtk [00:29:21] Found parallel - /usr/local/bin/parallel [00:29:21] Found freebayes - /usr/local/bin/freebayes [00:29:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:29:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:29:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:29:21] Found vcfuniq - /usr/local/bin/vcfuniq [00:29:21] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:29:21] Found gzip - /bin/gzip [00:29:21] Found vt - /usr/local/bin/vt [00:29:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:29:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:29:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:29:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:29:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:29:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:29:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:29:22] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:29:39] This is snippy 4.6.0
Show full stderr[00:29:39] This is snippy 4.6.0 [00:29:39] Written by Torsten Seemann [00:29:39] Obtained from https://github.com/tseemann/snippy [00:29:39] Detected operating system: linux [00:29:39] Enabling bundled linux tools. [00:29:39] Found bwa - /usr/local/bin/bwa [00:29:39] Found bcftools - /usr/local/bin/bcftools [00:29:39] Found samtools - /usr/local/bin/samtools [00:29:39] Found java - /usr/local/bin/java [00:29:39] Found snpEff - /usr/local/bin/snpEff [00:29:39] Found samclip - /usr/local/bin/samclip [00:29:39] Found seqtk - /usr/local/bin/seqtk [00:29:39] Found parallel - /usr/local/bin/parallel [00:29:39] Found freebayes - /usr/local/bin/freebayes [00:29:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:29:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:29:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:29:39] Found vcfuniq - /usr/local/bin/vcfuniq [00:29:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:29:39] Found gzip - /bin/gzip [00:29:39] Found vt - /usr/local/bin/vt [00:29:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:29:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:29:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:29:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:29:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:29:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:29:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:29:40] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:29:53] This is snippy 4.6.0
Show full stderr[00:29:53] This is snippy 4.6.0 [00:29:53] Written by Torsten Seemann [00:29:53] Obtained from https://github.com/tseemann/snippy [00:29:53] Detected operating system: linux [00:29:53] Enabling bundled linux tools. [00:29:53] Found bwa - /usr/local/bin/bwa [00:29:54] Found bcftools - /usr/local/bin/bcftools [00:29:54] Found samtools - /usr/local/bin/samtools [00:29:54] Found java - /usr/local/bin/java [00:29:54] Found snpEff - /usr/local/bin/snpEff [00:29:54] Found samclip - /usr/local/bin/samclip [00:29:54] Found seqtk - /usr/local/bin/seqtk [00:29:54] Found parallel - /usr/local/bin/parallel [00:29:54] Found freebayes - /usr/local/bin/freebayes [00:29:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:29:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:29:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:29:54] Found vcfuniq - /usr/local/bin/vcfuniq [00:29:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:29:54] Found gzip - /bin/gzip [00:29:54] Found vt - /usr/local/bin/vt [00:29:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:29:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:29:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:29:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:29:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:29:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:29:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:29:54] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:30:39] This is snippy 4.6.0
Show full stderr[00:30:39] This is snippy 4.6.0 [00:30:39] Written by Torsten Seemann [00:30:39] Obtained from https://github.com/tseemann/snippy [00:30:39] Detected operating system: linux [00:30:39] Enabling bundled linux tools. [00:30:39] Found bwa - /usr/local/bin/bwa [00:30:39] Found bcftools - /usr/local/bin/bcftools [00:30:39] Found samtools - /usr/local/bin/samtools [00:30:39] Found java - /usr/local/bin/java [00:30:39] Found snpEff - /usr/local/bin/snpEff [00:30:39] Found samclip - /usr/local/bin/samclip [00:30:39] Found seqtk - /usr/local/bin/seqtk [00:30:39] Found parallel - /usr/local/bin/parallel [00:30:39] Found freebayes - /usr/local/bin/freebayes [00:30:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:30:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:30:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:30:39] Found vcfuniq - /usr/local/bin/vcfuniq [00:30:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:30:39] Found gzip - /bin/gzip [00:30:39] Found vt - /usr/local/bin/vt [00:30:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:30:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:30:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:30:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:30:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:30:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:30:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:30:40] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:30:42] This is snippy 4.6.0
Show full stderr[00:30:42] This is snippy 4.6.0 [00:30:42] Written by Torsten Seemann [00:30:42] Obtained from https://github.com/tseemann/snippy [00:30:42] Detected operating system: linux [00:30:42] Enabling bundled linux tools. [00:30:42] Found bwa - /usr/local/bin/bwa [00:30:42] Found bcftools - /usr/local/bin/bcftools [00:30:42] Found samtools - /usr/local/bin/samtools [00:30:42] Found java - /usr/local/bin/java [00:30:42] Found snpEff - /usr/local/bin/snpEff [00:30:42] Found samclip - /usr/local/bin/samclip [00:30:42] Found seqtk - /usr/local/bin/seqtk [00:30:42] Found parallel - /usr/local/bin/parallel [00:30:42] Found freebayes - /usr/local/bin/freebayes [00:30:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:30:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:30:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:30:42] Found vcfuniq - /usr/local/bin/vcfuniq [00:30:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:30:42] Found gzip - /bin/gzip [00:30:42] Found vt - /usr/local/bin/vt [00:30:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:30:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:30:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:30:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:30:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:30:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:30:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:30:43] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:30:44] This is snippy 4.6.0
Show full stderr[00:30:44] This is snippy 4.6.0 [00:30:44] Written by Torsten Seemann [00:30:44] Obtained from https://github.com/tseemann/snippy [00:30:44] Detected operating system: linux [00:30:44] Enabling bundled linux tools. [00:30:44] Found bwa - /usr/local/bin/bwa [00:30:44] Found bcftools - /usr/local/bin/bcftools [00:30:44] Found samtools - /usr/local/bin/samtools [00:30:44] Found java - /usr/local/bin/java [00:30:44] Found snpEff - /usr/local/bin/snpEff [00:30:44] Found samclip - /usr/local/bin/samclip [00:30:44] Found seqtk - /usr/local/bin/seqtk [00:30:44] Found parallel - /usr/local/bin/parallel [00:30:44] Found freebayes - /usr/local/bin/freebayes [00:30:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:30:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:30:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:30:44] Found vcfuniq - /usr/local/bin/vcfuniq [00:30:44] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:30:44] Found gzip - /bin/gzip [00:30:44] Found vt - /usr/local/bin/vt [00:30:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:30:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:30:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:30:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:30:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:30:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:30:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:30:45] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:31:00] This is snippy 4.6.0
Show full stderr[00:31:00] This is snippy 4.6.0 [00:31:00] Written by Torsten Seemann [00:31:00] Obtained from https://github.com/tseemann/snippy [00:31:00] Detected operating system: linux [00:31:00] Enabling bundled linux tools. [00:31:00] Found bwa - /usr/local/bin/bwa [00:31:00] Found bcftools - /usr/local/bin/bcftools [00:31:00] Found samtools - /usr/local/bin/samtools [00:31:00] Found java - /usr/local/bin/java [00:31:00] Found snpEff - /usr/local/bin/snpEff [00:31:00] Found samclip - /usr/local/bin/samclip [00:31:00] Found seqtk - /usr/local/bin/seqtk [00:31:00] Found parallel - /usr/local/bin/parallel [00:31:00] Found freebayes - /usr/local/bin/freebayes [00:31:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:31:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:31:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:31:00] Found vcfuniq - /usr/local/bin/vcfuniq [00:31:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:31:00] Found gzip - /bin/gzip [00:31:00] Found vt - /usr/local/bin/vt [00:31:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:31:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:31:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:31:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:31:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:31:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:31:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:31:01] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:31:06] This is snippy 4.6.0
Show full stderr[00:31:06] This is snippy 4.6.0 [00:31:06] Written by Torsten Seemann [00:31:06] Obtained from https://github.com/tseemann/snippy [00:31:06] Detected operating system: linux [00:31:06] Enabling bundled linux tools. [00:31:06] Found bwa - /usr/local/bin/bwa [00:31:06] Found bcftools - /usr/local/bin/bcftools [00:31:06] Found samtools - /usr/local/bin/samtools [00:31:06] Found java - /usr/local/bin/java [00:31:06] Found snpEff - /usr/local/bin/snpEff [00:31:06] Found samclip - /usr/local/bin/samclip [00:31:06] Found seqtk - /usr/local/bin/seqtk [00:31:06] Found parallel - /usr/local/bin/parallel [00:31:06] Found freebayes - /usr/local/bin/freebayes [00:31:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:31:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:31:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:31:06] Found vcfuniq - /usr/local/bin/vcfuniq [00:31:06] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:31:06] Found gzip - /bin/gzip [00:31:06] Found vt - /usr/local/bin/vt [00:31:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:31:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:31:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:31:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:31:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:31:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:31:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:31:07] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:27:51] This is snippy 4.6.0
Show full stderr[00:27:51] This is snippy 4.6.0 [00:27:51] Written by Torsten Seemann [00:27:51] Obtained from https://github.com/tseemann/snippy [00:27:51] Detected operating system: linux [00:27:51] Enabling bundled linux tools. [00:27:51] Found bwa - /usr/local/bin/bwa [00:27:51] Found bcftools - /usr/local/bin/bcftools [00:27:51] Found samtools - /usr/local/bin/samtools [00:27:51] Found java - /usr/local/bin/java [00:27:51] Found snpEff - /usr/local/bin/snpEff [00:27:51] Found samclip - /usr/local/bin/samclip [00:27:51] Found seqtk - /usr/local/bin/seqtk [00:27:51] Found parallel - /usr/local/bin/parallel [00:27:51] Found freebayes - /usr/local/bin/freebayes [00:27:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:27:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:27:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:27:51] Found vcfuniq - /usr/local/bin/vcfuniq [00:27:51] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:27:51] Found gzip - /bin/gzip [00:27:51] Found vt - /usr/local/bin/vt [00:27:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:27:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:27:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:27:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:27:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:27:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:27:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:27:52] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:27:54] This is snippy 4.6.0
Show full stderr[00:27:54] This is snippy 4.6.0 [00:27:54] Written by Torsten Seemann [00:27:54] Obtained from https://github.com/tseemann/snippy [00:27:54] Detected operating system: linux [00:27:54] Enabling bundled linux tools. [00:27:54] Found bwa - /usr/local/bin/bwa [00:27:54] Found bcftools - /usr/local/bin/bcftools [00:27:54] Found samtools - /usr/local/bin/samtools [00:27:54] Found java - /usr/local/bin/java [00:27:54] Found snpEff - /usr/local/bin/snpEff [00:27:54] Found samclip - /usr/local/bin/samclip [00:27:55] Found seqtk - /usr/local/bin/seqtk [00:27:55] Found parallel - /usr/local/bin/parallel [00:27:55] Found freebayes - /usr/local/bin/freebayes [00:27:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:27:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:27:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:27:55] Found vcfuniq - /usr/local/bin/vcfuniq [00:27:55] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:27:55] Found gzip - /bin/gzip [00:27:55] Found vt - /usr/local/bin/vt [00:27:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:27:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:27:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:27:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:27:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:27:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:27:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:27:56] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:28:39] This is snippy 4.6.0
Show full stderr[00:28:39] This is snippy 4.6.0 [00:28:39] Written by Torsten Seemann [00:28:39] Obtained from https://github.com/tseemann/snippy [00:28:39] Detected operating system: linux [00:28:39] Enabling bundled linux tools. [00:28:39] Found bwa - /usr/local/bin/bwa [00:28:39] Found bcftools - /usr/local/bin/bcftools [00:28:39] Found samtools - /usr/local/bin/samtools [00:28:39] Found java - /usr/local/bin/java [00:28:39] Found snpEff - /usr/local/bin/snpEff [00:28:39] Found samclip - /usr/local/bin/samclip [00:28:39] Found seqtk - /usr/local/bin/seqtk [00:28:39] Found parallel - /usr/local/bin/parallel [00:28:39] Found freebayes - /usr/local/bin/freebayes [00:28:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:28:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:28:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:28:39] Found vcfuniq - /usr/local/bin/vcfuniq [00:28:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:28:39] Found gzip - /bin/gzip [00:28:39] Found vt - /usr/local/bin/vt [00:28:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:28:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:28:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:28:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:28:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:28:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:28:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:28:39] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:29:15] This is snippy 4.6.0
Show full stderr[00:29:15] This is snippy 4.6.0 [00:29:15] Written by Torsten Seemann [00:29:15] Obtained from https://github.com/tseemann/snippy [00:29:15] Detected operating system: linux [00:29:15] Enabling bundled linux tools. [00:29:15] Found bwa - /usr/local/bin/bwa [00:29:15] Found bcftools - /usr/local/bin/bcftools [00:29:15] Found samtools - /usr/local/bin/samtools [00:29:15] Found java - /usr/local/bin/java [00:29:15] Found snpEff - /usr/local/bin/snpEff [00:29:15] Found samclip - /usr/local/bin/samclip [00:29:15] Found seqtk - /usr/local/bin/seqtk [00:29:15] Found parallel - /usr/local/bin/parallel [00:29:15] Found freebayes - /usr/local/bin/freebayes [00:29:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:29:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:29:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:29:15] Found vcfuniq - /usr/local/bin/vcfuniq [00:29:15] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:29:15] Found gzip - /bin/gzip [00:29:15] Found vt - /usr/local/bin/vt [00:29:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:29:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:29:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:29:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:29:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:29:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:29:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:29:16] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:29:27] This is snippy 4.6.0
Show full stderr[00:29:27] This is snippy 4.6.0 [00:29:27] Written by Torsten Seemann [00:29:27] Obtained from https://github.com/tseemann/snippy [00:29:27] Detected operating system: linux [00:29:27] Enabling bundled linux tools. [00:29:27] Found bwa - /usr/local/bin/bwa [00:29:27] Found bcftools - /usr/local/bin/bcftools [00:29:27] Found samtools - /usr/local/bin/samtools [00:29:27] Found java - /usr/local/bin/java [00:29:27] Found snpEff - /usr/local/bin/snpEff [00:29:27] Found samclip - /usr/local/bin/samclip [00:29:27] Found seqtk - /usr/local/bin/seqtk [00:29:27] Found parallel - /usr/local/bin/parallel [00:29:27] Found freebayes - /usr/local/bin/freebayes [00:29:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:29:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:29:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:29:27] Found vcfuniq - /usr/local/bin/vcfuniq [00:29:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:29:27] Found gzip - /bin/gzip [00:29:27] Found vt - /usr/local/bin/vt [00:29:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:29:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:29:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:29:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:29:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:29:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:29:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:29:27] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:29:30] This is snippy 4.6.0
Show full stderr[00:29:30] This is snippy 4.6.0 [00:29:30] Written by Torsten Seemann [00:29:30] Obtained from https://github.com/tseemann/snippy [00:29:30] Detected operating system: linux [00:29:30] Enabling bundled linux tools. [00:29:30] Found bwa - /usr/local/bin/bwa [00:29:30] Found bcftools - /usr/local/bin/bcftools [00:29:30] Found samtools - /usr/local/bin/samtools [00:29:30] Found java - /usr/local/bin/java [00:29:30] Found snpEff - /usr/local/bin/snpEff [00:29:30] Found samclip - /usr/local/bin/samclip [00:29:30] Found seqtk - /usr/local/bin/seqtk [00:29:30] Found parallel - /usr/local/bin/parallel [00:29:30] Found freebayes - /usr/local/bin/freebayes [00:29:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:29:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:29:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:29:30] Found vcfuniq - /usr/local/bin/vcfuniq [00:29:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:29:30] Found gzip - /bin/gzip [00:29:30] Found vt - /usr/local/bin/vt [00:29:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:29:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:29:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:29:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:29:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:29:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:29:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:29:31] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:29:29] This is snippy 4.6.0
Show full stderr[00:29:29] This is snippy 4.6.0 [00:29:29] Written by Torsten Seemann [00:29:29] Obtained from https://github.com/tseemann/snippy [00:29:29] Detected operating system: linux [00:29:29] Enabling bundled linux tools. [00:29:29] Found bwa - /usr/local/bin/bwa [00:29:29] Found bcftools - /usr/local/bin/bcftools [00:29:29] Found samtools - /usr/local/bin/samtools [00:29:29] Found java - /usr/local/bin/java [00:29:29] Found snpEff - /usr/local/bin/snpEff [00:29:30] Found samclip - /usr/local/bin/samclip [00:29:30] Found seqtk - /usr/local/bin/seqtk [00:29:30] Found parallel - /usr/local/bin/parallel [00:29:30] Found freebayes - /usr/local/bin/freebayes [00:29:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:29:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:29:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:29:30] Found vcfuniq - /usr/local/bin/vcfuniq [00:29:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:29:30] Found gzip - /bin/gzip [00:29:30] Found vt - /usr/local/bin/vt [00:29:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:29:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:29:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:29:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:29:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:29:30] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:29:30] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:29:30] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:30:12] This is snippy 4.6.0
Show full stderr[00:30:12] This is snippy 4.6.0 [00:30:12] Written by Torsten Seemann [00:30:12] Obtained from https://github.com/tseemann/snippy [00:30:12] Detected operating system: linux [00:30:12] Enabling bundled linux tools. [00:30:12] Found bwa - /usr/local/bin/bwa [00:30:12] Found bcftools - /usr/local/bin/bcftools [00:30:12] Found samtools - /usr/local/bin/samtools [00:30:12] Found java - /usr/local/bin/java [00:30:12] Found snpEff - /usr/local/bin/snpEff [00:30:12] Found samclip - /usr/local/bin/samclip [00:30:12] Found seqtk - /usr/local/bin/seqtk [00:30:12] Found parallel - /usr/local/bin/parallel [00:30:12] Found freebayes - /usr/local/bin/freebayes [00:30:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:30:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:30:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:30:12] Found vcfuniq - /usr/local/bin/vcfuniq [00:30:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:30:12] Found gzip - /bin/gzip [00:30:12] Found vt - /usr/local/bin/vt [00:30:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:30:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:30:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:30:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:30:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:30:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:30:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:30:13] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:30:24] This is snippy 4.6.0
Show full stderr[00:30:24] This is snippy 4.6.0 [00:30:24] Written by Torsten Seemann [00:30:24] Obtained from https://github.com/tseemann/snippy [00:30:24] Detected operating system: linux [00:30:24] Enabling bundled linux tools. [00:30:24] Found bwa - /usr/local/bin/bwa [00:30:24] Found bcftools - /usr/local/bin/bcftools [00:30:24] Found samtools - /usr/local/bin/samtools [00:30:24] Found java - /usr/local/bin/java [00:30:24] Found snpEff - /usr/local/bin/snpEff [00:30:24] Found samclip - /usr/local/bin/samclip [00:30:24] Found seqtk - /usr/local/bin/seqtk [00:30:24] Found parallel - /usr/local/bin/parallel [00:30:24] Found freebayes - /usr/local/bin/freebayes [00:30:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:30:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:30:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:30:24] Found vcfuniq - /usr/local/bin/vcfuniq [00:30:24] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:30:24] Found gzip - /bin/gzip [00:30:24] Found vt - /usr/local/bin/vt [00:30:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:30:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:30:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:30:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:30:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:30:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:30:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:30:25] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:31:44] This is snippy 4.6.0
Show full stderr[00:31:44] This is snippy 4.6.0 [00:31:44] Written by Torsten Seemann [00:31:44] Obtained from https://github.com/tseemann/snippy [00:31:44] Detected operating system: linux [00:31:44] Enabling bundled linux tools. [00:31:44] Found bwa - /usr/local/bin/bwa [00:31:44] Found bcftools - /usr/local/bin/bcftools [00:31:44] Found samtools - /usr/local/bin/samtools [00:31:44] Found java - /usr/local/bin/java [00:31:44] Found snpEff - /usr/local/bin/snpEff [00:31:44] Found samclip - /usr/local/bin/samclip [00:31:44] Found seqtk - /usr/local/bin/seqtk [00:31:44] Found parallel - /usr/local/bin/parallel [00:31:44] Found freebayes - /usr/local/bin/freebayes [00:31:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:31:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:31:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:31:44] Found vcfuniq - /usr/local/bin/vcfuniq [00:31:44] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:31:44] Found gzip - /bin/gzip [00:31:44] Found vt - /usr/local/bin/vt [00:31:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:31:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:31:44] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:31:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:31:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:31:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:31:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:31:45] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:31:51] This is snippy 4.6.0
Show full stderr[00:31:51] This is snippy 4.6.0 [00:31:51] Written by Torsten Seemann [00:31:51] Obtained from https://github.com/tseemann/snippy [00:31:51] Detected operating system: linux [00:31:51] Enabling bundled linux tools. [00:31:51] Found bwa - /usr/local/bin/bwa [00:31:51] Found bcftools - /usr/local/bin/bcftools [00:31:51] Found samtools - /usr/local/bin/samtools [00:31:51] Found java - /usr/local/bin/java [00:31:51] Found snpEff - /usr/local/bin/snpEff [00:31:51] Found samclip - /usr/local/bin/samclip [00:31:51] Found seqtk - /usr/local/bin/seqtk [00:31:51] Found parallel - /usr/local/bin/parallel [00:31:51] Found freebayes - /usr/local/bin/freebayes [00:31:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:31:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:31:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:31:51] Found vcfuniq - /usr/local/bin/vcfuniq [00:31:51] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:31:51] Found gzip - /bin/gzip [00:31:51] Found vt - /usr/local/bin/vt [00:31:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:31:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:31:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:31:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:31:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:31:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:31:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:31:52] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:32:31] This is snippy 4.6.0
Show full stderr[00:32:31] This is snippy 4.6.0 [00:32:31] Written by Torsten Seemann [00:32:31] Obtained from https://github.com/tseemann/snippy [00:32:31] Detected operating system: linux [00:32:31] Enabling bundled linux tools. [00:32:31] Found bwa - /usr/local/bin/bwa [00:32:31] Found bcftools - /usr/local/bin/bcftools [00:32:31] Found samtools - /usr/local/bin/samtools [00:32:31] Found java - /usr/local/bin/java [00:32:31] Found snpEff - /usr/local/bin/snpEff [00:32:31] Found samclip - /usr/local/bin/samclip [00:32:31] Found seqtk - /usr/local/bin/seqtk [00:32:31] Found parallel - /usr/local/bin/parallel [00:32:31] Found freebayes - /usr/local/bin/freebayes [00:32:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:32:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:32:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:32:31] Found vcfuniq - /usr/local/bin/vcfuniq [00:32:31] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:32:31] Found gzip - /bin/gzip [00:32:31] Found vt - /usr/local/bin/vt [00:32:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:32:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:32:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:32:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:32:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:32:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:32:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:32:32] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:33:12] This is snippy 4.6.0
Show full stderr[00:33:12] This is snippy 4.6.0 [00:33:12] Written by Torsten Seemann [00:33:12] Obtained from https://github.com/tseemann/snippy [00:33:12] Detected operating system: linux [00:33:12] Enabling bundled linux tools. [00:33:12] Found bwa - /usr/local/bin/bwa [00:33:12] Found bcftools - /usr/local/bin/bcftools [00:33:12] Found samtools - /usr/local/bin/samtools [00:33:12] Found java - /usr/local/bin/java [00:33:12] Found snpEff - /usr/local/bin/snpEff [00:33:12] Found samclip - /usr/local/bin/samclip [00:33:12] Found seqtk - /usr/local/bin/seqtk [00:33:12] Found parallel - /usr/local/bin/parallel [00:33:12] Found freebayes - /usr/local/bin/freebayes [00:33:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:33:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:33:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:33:12] Found vcfuniq - /usr/local/bin/vcfuniq [00:33:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:33:12] Found gzip - /bin/gzip [00:33:12] Found vt - /usr/local/bin/vt [00:33:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:33:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:33:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:33:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:33:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:33:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:33:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:33:13] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:59:04] This is snippy 4.6.0
Show full stderr[00:59:04] This is snippy 4.6.0 [00:59:04] Written by Torsten Seemann [00:59:04] Obtained from https://github.com/tseemann/snippy [00:59:04] Detected operating system: linux [00:59:04] Enabling bundled linux tools. [00:59:04] Found bwa - /usr/local/bin/bwa [00:59:04] Found bcftools - /usr/local/bin/bcftools [00:59:04] Found samtools - /usr/local/bin/samtools [00:59:04] Found java - /usr/local/bin/java [00:59:04] Found snpEff - /usr/local/bin/snpEff [00:59:04] Found samclip - /usr/local/bin/samclip [00:59:04] Found seqtk - /usr/local/bin/seqtk [00:59:04] Found parallel - /usr/local/bin/parallel [00:59:04] Found freebayes - /usr/local/bin/freebayes [00:59:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:59:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:59:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:59:04] Found vcfuniq - /usr/local/bin/vcfuniq [00:59:04] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:59:04] Found gzip - /bin/gzip [00:59:04] Found vt - /usr/local/bin/vt [00:59:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:59:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:59:05] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:59:05] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:59:05] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:59:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:59:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:59:05] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:04:33] This is snippy 4.6.0
Show full stderr[01:04:33] This is snippy 4.6.0 [01:04:33] Written by Torsten Seemann [01:04:33] Obtained from https://github.com/tseemann/snippy [01:04:33] Detected operating system: linux [01:04:33] Enabling bundled linux tools. [01:04:33] Found bwa - /usr/local/bin/bwa [01:04:33] Found bcftools - /usr/local/bin/bcftools [01:04:33] Found samtools - /usr/local/bin/samtools [01:04:33] Found java - /usr/local/bin/java [01:04:33] Found snpEff - /usr/local/bin/snpEff [01:04:33] Found samclip - /usr/local/bin/samclip [01:04:33] Found seqtk - /usr/local/bin/seqtk [01:04:33] Found parallel - /usr/local/bin/parallel [01:04:33] Found freebayes - /usr/local/bin/freebayes [01:04:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:04:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:04:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:04:33] Found vcfuniq - /usr/local/bin/vcfuniq [01:04:33] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:04:33] Found gzip - /bin/gzip [01:04:33] Found vt - /usr/local/bin/vt [01:04:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:04:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:04:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:04:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:04:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:04:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:04:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:04:35] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:04:51] This is snippy 4.6.0
Show full stderr[01:04:51] This is snippy 4.6.0 [01:04:51] Written by Torsten Seemann [01:04:51] Obtained from https://github.com/tseemann/snippy [01:04:51] Detected operating system: linux [01:04:51] Enabling bundled linux tools. [01:04:51] Found bwa - /usr/local/bin/bwa [01:04:51] Found bcftools - /usr/local/bin/bcftools [01:04:51] Found samtools - /usr/local/bin/samtools [01:04:51] Found java - /usr/local/bin/java [01:04:51] Found snpEff - /usr/local/bin/snpEff [01:04:51] Found samclip - /usr/local/bin/samclip [01:04:51] Found seqtk - /usr/local/bin/seqtk [01:04:51] Found parallel - /usr/local/bin/parallel [01:04:51] Found freebayes - /usr/local/bin/freebayes [01:04:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:04:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:04:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:04:51] Found vcfuniq - /usr/local/bin/vcfuniq [01:04:51] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:04:52] Found gzip - /bin/gzip [01:04:52] Found vt - /usr/local/bin/vt [01:04:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:04:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:04:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:04:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:04:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:04:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:04:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:04:53] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:05:30] This is snippy 4.6.0
Show full stderr[01:05:30] This is snippy 4.6.0 [01:05:30] Written by Torsten Seemann [01:05:30] Obtained from https://github.com/tseemann/snippy [01:05:30] Detected operating system: linux [01:05:30] Enabling bundled linux tools. [01:05:30] Found bwa - /usr/local/bin/bwa [01:05:31] Found bcftools - /usr/local/bin/bcftools [01:05:31] Found samtools - /usr/local/bin/samtools [01:05:31] Found java - /usr/local/bin/java [01:05:31] Found snpEff - /usr/local/bin/snpEff [01:05:31] Found samclip - /usr/local/bin/samclip [01:05:31] Found seqtk - /usr/local/bin/seqtk [01:05:31] Found parallel - /usr/local/bin/parallel [01:05:31] Found freebayes - /usr/local/bin/freebayes [01:05:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:05:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:05:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:05:31] Found vcfuniq - /usr/local/bin/vcfuniq [01:05:31] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:05:31] Found gzip - /bin/gzip [01:05:31] Found vt - /usr/local/bin/vt [01:05:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:05:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:05:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:05:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:05:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:05:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:05:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:05:33] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:07:19] This is snippy 4.6.0
Show full stderr[01:07:19] This is snippy 4.6.0 [01:07:19] Written by Torsten Seemann [01:07:19] Obtained from https://github.com/tseemann/snippy [01:07:19] Detected operating system: linux [01:07:19] Enabling bundled linux tools. [01:07:19] Found bwa - /usr/local/bin/bwa [01:07:19] Found bcftools - /usr/local/bin/bcftools [01:07:19] Found samtools - /usr/local/bin/samtools [01:07:19] Found java - /usr/local/bin/java [01:07:19] Found snpEff - /usr/local/bin/snpEff [01:07:19] Found samclip - /usr/local/bin/samclip [01:07:19] Found seqtk - /usr/local/bin/seqtk [01:07:19] Found parallel - /usr/local/bin/parallel [01:07:19] Found freebayes - /usr/local/bin/freebayes [01:07:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:07:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:07:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:07:19] Found vcfuniq - /usr/local/bin/vcfuniq [01:07:19] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:07:19] Found gzip - /bin/gzip [01:07:19] Found vt - /usr/local/bin/vt [01:07:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:07:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:07:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:07:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:07:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:07:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:07:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:07:20] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:13:42] This is snippy 4.6.0
Show full stderr[01:13:42] This is snippy 4.6.0 [01:13:42] Written by Torsten Seemann [01:13:42] Obtained from https://github.com/tseemann/snippy [01:13:42] Detected operating system: linux [01:13:42] Enabling bundled linux tools. [01:13:42] Found bwa - /usr/local/bin/bwa [01:13:42] Found bcftools - /usr/local/bin/bcftools [01:13:42] Found samtools - /usr/local/bin/samtools [01:13:42] Found java - /usr/local/bin/java [01:13:42] Found snpEff - /usr/local/bin/snpEff [01:13:42] Found samclip - /usr/local/bin/samclip [01:13:42] Found seqtk - /usr/local/bin/seqtk [01:13:42] Found parallel - /usr/local/bin/parallel [01:13:42] Found freebayes - /usr/local/bin/freebayes [01:13:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:13:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:13:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:13:42] Found vcfuniq - /usr/local/bin/vcfuniq [01:13:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:13:42] Found gzip - /bin/gzip [01:13:42] Found vt - /usr/local/bin/vt [01:13:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:13:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:13:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:13:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:13:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:13:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:13:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:13:43] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:14:06] This is snippy 4.6.0
Show full stderr[01:14:06] This is snippy 4.6.0 [01:14:06] Written by Torsten Seemann [01:14:06] Obtained from https://github.com/tseemann/snippy [01:14:06] Detected operating system: linux [01:14:06] Enabling bundled linux tools. [01:14:06] Found bwa - /usr/local/bin/bwa [01:14:06] Found bcftools - /usr/local/bin/bcftools [01:14:06] Found samtools - /usr/local/bin/samtools [01:14:06] Found java - /usr/local/bin/java [01:14:06] Found snpEff - /usr/local/bin/snpEff [01:14:06] Found samclip - /usr/local/bin/samclip [01:14:06] Found seqtk - /usr/local/bin/seqtk [01:14:06] Found parallel - /usr/local/bin/parallel [01:14:06] Found freebayes - /usr/local/bin/freebayes [01:14:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:14:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:14:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:14:06] Found vcfuniq - /usr/local/bin/vcfuniq [01:14:06] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:14:06] Found gzip - /bin/gzip [01:14:06] Found vt - /usr/local/bin/vt [01:14:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:14:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:14:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:14:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:14:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:14:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:14:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:14:07] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:15:39] This is snippy 4.6.0
Show full stderr[01:15:39] This is snippy 4.6.0 [01:15:39] Written by Torsten Seemann [01:15:39] Obtained from https://github.com/tseemann/snippy [01:15:39] Detected operating system: linux [01:15:39] Enabling bundled linux tools. [01:15:39] Found bwa - /usr/local/bin/bwa [01:15:39] Found bcftools - /usr/local/bin/bcftools [01:15:39] Found samtools - /usr/local/bin/samtools [01:15:39] Found java - /usr/local/bin/java [01:15:39] Found snpEff - /usr/local/bin/snpEff [01:15:39] Found samclip - /usr/local/bin/samclip [01:15:39] Found seqtk - /usr/local/bin/seqtk [01:15:39] Found parallel - /usr/local/bin/parallel [01:15:39] Found freebayes - /usr/local/bin/freebayes [01:15:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:15:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:15:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:15:39] Found vcfuniq - /usr/local/bin/vcfuniq [01:15:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:15:39] Found gzip - /bin/gzip [01:15:39] Found vt - /usr/local/bin/vt [01:15:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:15:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:15:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:15:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:15:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:15:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:15:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:15:40] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:20:52] This is snippy 4.6.0
Show full stderr[01:20:52] This is snippy 4.6.0 [01:20:52] Written by Torsten Seemann [01:20:52] Obtained from https://github.com/tseemann/snippy [01:20:52] Detected operating system: linux [01:20:52] Enabling bundled linux tools. [01:20:52] Found bwa - /usr/local/bin/bwa [01:20:53] Found bcftools - /usr/local/bin/bcftools [01:20:53] Found samtools - /usr/local/bin/samtools [01:20:53] Found java - /usr/local/bin/java [01:20:53] Found snpEff - /usr/local/bin/snpEff [01:20:53] Found samclip - /usr/local/bin/samclip [01:20:53] Found seqtk - /usr/local/bin/seqtk [01:20:53] Found parallel - /usr/local/bin/parallel [01:20:53] Found freebayes - /usr/local/bin/freebayes [01:20:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:20:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:20:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:20:53] Found vcfuniq - /usr/local/bin/vcfuniq [01:20:53] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:20:53] Found gzip - /bin/gzip [01:20:53] Found vt - /usr/local/bin/vt [01:20:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:20:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:20:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:20:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:20:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:20:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:20:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:20:54] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:24:37] This is snippy 4.6.0
Show full stderr[01:24:37] This is snippy 4.6.0 [01:24:37] Written by Torsten Seemann [01:24:37] Obtained from https://github.com/tseemann/snippy [01:24:37] Detected operating system: linux [01:24:37] Enabling bundled linux tools. [01:24:37] Found bwa - /usr/local/bin/bwa [01:24:37] Found bcftools - /usr/local/bin/bcftools [01:24:37] Found samtools - /usr/local/bin/samtools [01:24:37] Found java - /usr/local/bin/java [01:24:37] Found snpEff - /usr/local/bin/snpEff [01:24:37] Found samclip - /usr/local/bin/samclip [01:24:37] Found seqtk - /usr/local/bin/seqtk [01:24:37] Found parallel - /usr/local/bin/parallel [01:24:37] Found freebayes - /usr/local/bin/freebayes [01:24:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:24:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:24:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:24:37] Found vcfuniq - /usr/local/bin/vcfuniq [01:24:37] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:24:37] Found gzip - /bin/gzip [01:24:37] Found vt - /usr/local/bin/vt [01:24:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:24:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:24:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:24:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:24:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:24:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:24:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:24:38] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:30:37] This is snippy 4.6.0
Show full stderr[01:30:37] This is snippy 4.6.0 [01:30:37] Written by Torsten Seemann [01:30:37] Obtained from https://github.com/tseemann/snippy [01:30:37] Detected operating system: linux [01:30:37] Enabling bundled linux tools. [01:30:37] Found bwa - /usr/local/bin/bwa [01:30:37] Found bcftools - /usr/local/bin/bcftools [01:30:37] Found samtools - /usr/local/bin/samtools [01:30:37] Found java - /usr/local/bin/java [01:30:37] Found snpEff - /usr/local/bin/snpEff [01:30:37] Found samclip - /usr/local/bin/samclip [01:30:37] Found seqtk - /usr/local/bin/seqtk [01:30:37] Found parallel - /usr/local/bin/parallel [01:30:37] Found freebayes - /usr/local/bin/freebayes [01:30:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:30:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:30:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:30:37] Found vcfuniq - /usr/local/bin/vcfuniq [01:30:37] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:30:37] Found gzip - /bin/gzip [01:30:37] Found vt - /usr/local/bin/vt [01:30:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:30:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:30:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:30:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:30:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:30:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:30:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:30:38] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:21:42] This is snippy 4.6.0
Show full stderr[01:21:42] This is snippy 4.6.0 [01:21:42] Written by Torsten Seemann [01:21:42] Obtained from https://github.com/tseemann/snippy [01:21:42] Detected operating system: linux [01:21:42] Enabling bundled linux tools. [01:21:42] Found bwa - /usr/local/bin/bwa [01:21:42] Found bcftools - /usr/local/bin/bcftools [01:21:42] Found samtools - /usr/local/bin/samtools [01:21:42] Found java - /usr/local/bin/java [01:21:42] Found snpEff - /usr/local/bin/snpEff [01:21:42] Found samclip - /usr/local/bin/samclip [01:21:42] Found seqtk - /usr/local/bin/seqtk [01:21:42] Found parallel - /usr/local/bin/parallel [01:21:42] Found freebayes - /usr/local/bin/freebayes [01:21:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:21:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:21:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:21:42] Found vcfuniq - /usr/local/bin/vcfuniq [01:21:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:21:42] Found gzip - /bin/gzip [01:21:42] Found vt - /usr/local/bin/vt [01:21:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:21:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:21:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:21:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:21:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:21:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:21:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:21:43] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:22:22] This is snippy 4.6.0
Show full stderr[01:22:22] This is snippy 4.6.0 [01:22:22] Written by Torsten Seemann [01:22:22] Obtained from https://github.com/tseemann/snippy [01:22:22] Detected operating system: linux [01:22:22] Enabling bundled linux tools. [01:22:22] Found bwa - /usr/local/bin/bwa [01:22:22] Found bcftools - /usr/local/bin/bcftools [01:22:22] Found samtools - /usr/local/bin/samtools [01:22:22] Found java - /usr/local/bin/java [01:22:22] Found snpEff - /usr/local/bin/snpEff [01:22:22] Found samclip - /usr/local/bin/samclip [01:22:22] Found seqtk - /usr/local/bin/seqtk [01:22:22] Found parallel - /usr/local/bin/parallel [01:22:22] Found freebayes - /usr/local/bin/freebayes [01:22:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:22:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:22:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:22:22] Found vcfuniq - /usr/local/bin/vcfuniq [01:22:22] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:22:22] Found gzip - /bin/gzip [01:22:22] Found vt - /usr/local/bin/vt [01:22:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:22:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:22:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:22:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:22:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:22:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:22:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:22:23] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:22:39] This is snippy 4.6.0
Show full stderr[01:22:39] This is snippy 4.6.0 [01:22:39] Written by Torsten Seemann [01:22:39] Obtained from https://github.com/tseemann/snippy [01:22:39] Detected operating system: linux [01:22:39] Enabling bundled linux tools. [01:22:39] Found bwa - /usr/local/bin/bwa [01:22:39] Found bcftools - /usr/local/bin/bcftools [01:22:39] Found samtools - /usr/local/bin/samtools [01:22:39] Found java - /usr/local/bin/java [01:22:39] Found snpEff - /usr/local/bin/snpEff [01:22:39] Found samclip - /usr/local/bin/samclip [01:22:39] Found seqtk - /usr/local/bin/seqtk [01:22:39] Found parallel - /usr/local/bin/parallel [01:22:39] Found freebayes - /usr/local/bin/freebayes [01:22:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:22:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:22:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:22:39] Found vcfuniq - /usr/local/bin/vcfuniq [01:22:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:22:39] Found gzip - /bin/gzip [01:22:39] Found vt - /usr/local/bin/vt [01:22:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:22:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:22:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:22:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:22:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:22:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:22:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:22:40] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:22:54] This is snippy 4.6.0
Show full stderr[01:22:54] This is snippy 4.6.0 [01:22:54] Written by Torsten Seemann [01:22:54] Obtained from https://github.com/tseemann/snippy [01:22:54] Detected operating system: linux [01:22:54] Enabling bundled linux tools. [01:22:54] Found bwa - /usr/local/bin/bwa [01:22:54] Found bcftools - /usr/local/bin/bcftools [01:22:54] Found samtools - /usr/local/bin/samtools [01:22:54] Found java - /usr/local/bin/java [01:22:54] Found snpEff - /usr/local/bin/snpEff [01:22:54] Found samclip - /usr/local/bin/samclip [01:22:54] Found seqtk - /usr/local/bin/seqtk [01:22:54] Found parallel - /usr/local/bin/parallel [01:22:54] Found freebayes - /usr/local/bin/freebayes [01:22:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:22:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:22:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:22:54] Found vcfuniq - /usr/local/bin/vcfuniq [01:22:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:22:54] Found gzip - /bin/gzip [01:22:54] Found vt - /usr/local/bin/vt [01:22:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:22:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:22:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:22:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:22:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:22:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:22:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:22:55] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:29:09] This is snippy 4.6.0
Show full stderr[00:29:09] This is snippy 4.6.0 [00:29:09] Written by Torsten Seemann [00:29:09] Obtained from https://github.com/tseemann/snippy [00:29:09] Detected operating system: linux [00:29:09] Enabling bundled linux tools. [00:29:09] Found bwa - /usr/local/bin/bwa [00:29:09] Found bcftools - /usr/local/bin/bcftools [00:29:09] Found samtools - /usr/local/bin/samtools [00:29:09] Found java - /usr/local/bin/java [00:29:09] Found snpEff - /usr/local/bin/snpEff [00:29:09] Found samclip - /usr/local/bin/samclip [00:29:09] Found seqtk - /usr/local/bin/seqtk [00:29:09] Found parallel - /usr/local/bin/parallel [00:29:09] Found freebayes - /usr/local/bin/freebayes [00:29:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:29:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:29:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:29:09] Found vcfuniq - /usr/local/bin/vcfuniq [00:29:09] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:29:09] Found gzip - /bin/gzip [00:29:09] Found vt - /usr/local/bin/vt [00:29:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:29:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:29:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:29:11] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:29:11] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:29:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:29:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:29:13] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:32:45] This is snippy 4.6.0
Show full stderr[00:32:45] This is snippy 4.6.0 [00:32:45] Written by Torsten Seemann [00:32:45] Obtained from https://github.com/tseemann/snippy [00:32:45] Detected operating system: linux [00:32:45] Enabling bundled linux tools. [00:32:45] Found bwa - /usr/local/bin/bwa [00:32:45] Found bcftools - /usr/local/bin/bcftools [00:32:45] Found samtools - /usr/local/bin/samtools [00:32:45] Found java - /usr/local/bin/java [00:32:45] Found snpEff - /usr/local/bin/snpEff [00:32:45] Found samclip - /usr/local/bin/samclip [00:32:45] Found seqtk - /usr/local/bin/seqtk [00:32:45] Found parallel - /usr/local/bin/parallel [00:32:45] Found freebayes - /usr/local/bin/freebayes [00:32:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:32:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:32:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:32:45] Found vcfuniq - /usr/local/bin/vcfuniq [00:32:45] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:32:45] Found gzip - /bin/gzip [00:32:45] Found vt - /usr/local/bin/vt [00:32:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:32:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:32:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:32:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:32:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:32:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:32:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:32:46] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:33:09] This is snippy 4.6.0
Show full stderr[00:33:09] This is snippy 4.6.0 [00:33:09] Written by Torsten Seemann [00:33:09] Obtained from https://github.com/tseemann/snippy [00:33:09] Detected operating system: linux [00:33:09] Enabling bundled linux tools. [00:33:09] Found bwa - /usr/local/bin/bwa [00:33:09] Found bcftools - /usr/local/bin/bcftools [00:33:09] Found samtools - /usr/local/bin/samtools [00:33:09] Found java - /usr/local/bin/java [00:33:09] Found snpEff - /usr/local/bin/snpEff [00:33:09] Found samclip - /usr/local/bin/samclip [00:33:09] Found seqtk - /usr/local/bin/seqtk [00:33:09] Found parallel - /usr/local/bin/parallel [00:33:09] Found freebayes - /usr/local/bin/freebayes [00:33:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:33:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:33:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:33:09] Found vcfuniq - /usr/local/bin/vcfuniq [00:33:09] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:33:09] Found gzip - /bin/gzip [00:33:09] Found vt - /usr/local/bin/vt [00:33:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:33:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:33:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:33:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:33:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:33:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:33:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:33:10] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:33:44] This is snippy 4.6.0
Show full stderr[00:33:44] This is snippy 4.6.0 [00:33:44] Written by Torsten Seemann [00:33:44] Obtained from https://github.com/tseemann/snippy [00:33:44] Detected operating system: linux [00:33:44] Enabling bundled linux tools. [00:33:44] Found bwa - /usr/local/bin/bwa [00:33:44] Found bcftools - /usr/local/bin/bcftools [00:33:44] Found samtools - /usr/local/bin/samtools [00:33:44] Found java - /usr/local/bin/java [00:33:44] Found snpEff - /usr/local/bin/snpEff [00:33:44] Found samclip - /usr/local/bin/samclip [00:33:44] Found seqtk - /usr/local/bin/seqtk [00:33:44] Found parallel - /usr/local/bin/parallel [00:33:44] Found freebayes - /usr/local/bin/freebayes [00:33:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:33:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:33:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:33:44] Found vcfuniq - /usr/local/bin/vcfuniq [00:33:44] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:33:44] Found gzip - /bin/gzip [00:33:44] Found vt - /usr/local/bin/vt [00:33:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:33:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:33:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:33:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:33:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:33:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:33:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:33:46] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:34:24] This is snippy 4.6.0
Show full stderr[00:34:24] This is snippy 4.6.0 [00:34:24] Written by Torsten Seemann [00:34:24] Obtained from https://github.com/tseemann/snippy [00:34:24] Detected operating system: linux [00:34:24] Enabling bundled linux tools. [00:34:24] Found bwa - /usr/local/bin/bwa [00:34:24] Found bcftools - /usr/local/bin/bcftools [00:34:24] Found samtools - /usr/local/bin/samtools [00:34:24] Found java - /usr/local/bin/java [00:34:24] Found snpEff - /usr/local/bin/snpEff [00:34:24] Found samclip - /usr/local/bin/samclip [00:34:24] Found seqtk - /usr/local/bin/seqtk [00:34:24] Found parallel - /usr/local/bin/parallel [00:34:24] Found freebayes - /usr/local/bin/freebayes [00:34:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:34:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:34:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:34:24] Found vcfuniq - /usr/local/bin/vcfuniq [00:34:24] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:34:24] Found gzip - /bin/gzip [00:34:24] Found vt - /usr/local/bin/vt [00:34:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:34:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:34:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:34:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:34:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:34:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:34:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:34:25] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:34:27] This is snippy 4.6.0
Show full stderr[00:34:27] This is snippy 4.6.0 [00:34:27] Written by Torsten Seemann [00:34:27] Obtained from https://github.com/tseemann/snippy [00:34:27] Detected operating system: linux [00:34:27] Enabling bundled linux tools. [00:34:27] Found bwa - /usr/local/bin/bwa [00:34:27] Found bcftools - /usr/local/bin/bcftools [00:34:27] Found samtools - /usr/local/bin/samtools [00:34:27] Found java - /usr/local/bin/java [00:34:27] Found snpEff - /usr/local/bin/snpEff [00:34:27] Found samclip - /usr/local/bin/samclip [00:34:27] Found seqtk - /usr/local/bin/seqtk [00:34:27] Found parallel - /usr/local/bin/parallel [00:34:27] Found freebayes - /usr/local/bin/freebayes [00:34:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:34:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:34:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:34:27] Found vcfuniq - /usr/local/bin/vcfuniq [00:34:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:34:27] Found gzip - /bin/gzip [00:34:27] Found vt - /usr/local/bin/vt [00:34:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:34:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:34:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:34:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:34:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:34:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:34:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:34:28] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:34:33] This is snippy 4.6.0
Show full stderr[00:34:33] This is snippy 4.6.0 [00:34:33] Written by Torsten Seemann [00:34:33] Obtained from https://github.com/tseemann/snippy [00:34:33] Detected operating system: linux [00:34:33] Enabling bundled linux tools. [00:34:33] Found bwa - /usr/local/bin/bwa [00:34:33] Found bcftools - /usr/local/bin/bcftools [00:34:33] Found samtools - /usr/local/bin/samtools [00:34:33] Found java - /usr/local/bin/java [00:34:33] Found snpEff - /usr/local/bin/snpEff [00:34:33] Found samclip - /usr/local/bin/samclip [00:34:33] Found seqtk - /usr/local/bin/seqtk [00:34:33] Found parallel - /usr/local/bin/parallel [00:34:33] Found freebayes - /usr/local/bin/freebayes [00:34:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:34:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:34:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:34:33] Found vcfuniq - /usr/local/bin/vcfuniq [00:34:33] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:34:33] Found gzip - /bin/gzip [00:34:33] Found vt - /usr/local/bin/vt [00:34:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:34:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:34:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:34:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:34:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:34:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:34:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:34:34] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:35:09] This is snippy 4.6.0
Show full stderr[00:35:09] This is snippy 4.6.0 [00:35:09] Written by Torsten Seemann [00:35:09] Obtained from https://github.com/tseemann/snippy [00:35:09] Detected operating system: linux [00:35:09] Enabling bundled linux tools. [00:35:09] Found bwa - /usr/local/bin/bwa [00:35:09] Found bcftools - /usr/local/bin/bcftools [00:35:09] Found samtools - /usr/local/bin/samtools [00:35:09] Found java - /usr/local/bin/java [00:35:09] Found snpEff - /usr/local/bin/snpEff [00:35:09] Found samclip - /usr/local/bin/samclip [00:35:09] Found seqtk - /usr/local/bin/seqtk [00:35:09] Found parallel - /usr/local/bin/parallel [00:35:09] Found freebayes - /usr/local/bin/freebayes [00:35:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:35:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:35:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:35:10] Found vcfuniq - /usr/local/bin/vcfuniq [00:35:10] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:35:10] Found gzip - /bin/gzip [00:35:10] Found vt - /usr/local/bin/vt [00:35:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:35:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:35:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:35:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:35:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:35:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:35:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:35:11] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:38:57] This is snippy 4.6.0
Show full stderr[00:38:57] This is snippy 4.6.0 [00:38:57] Written by Torsten Seemann [00:38:57] Obtained from https://github.com/tseemann/snippy [00:38:57] Detected operating system: linux [00:38:57] Enabling bundled linux tools. [00:38:57] Found bwa - /usr/local/bin/bwa [00:38:57] Found bcftools - /usr/local/bin/bcftools [00:38:57] Found samtools - /usr/local/bin/samtools [00:38:57] Found java - /usr/local/bin/java [00:38:57] Found snpEff - /usr/local/bin/snpEff [00:38:57] Found samclip - /usr/local/bin/samclip [00:38:57] Found seqtk - /usr/local/bin/seqtk [00:38:57] Found parallel - /usr/local/bin/parallel [00:38:57] Found freebayes - /usr/local/bin/freebayes [00:38:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:38:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:38:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:38:57] Found vcfuniq - /usr/local/bin/vcfuniq [00:38:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:38:57] Found gzip - /bin/gzip [00:38:57] Found vt - /usr/local/bin/vt [00:38:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:38:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:38:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:38:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:38:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:38:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:38:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:38:58] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:43:46] This is snippy 4.6.0
Show full stderr[00:43:46] This is snippy 4.6.0 [00:43:46] Written by Torsten Seemann [00:43:46] Obtained from https://github.com/tseemann/snippy [00:43:46] Detected operating system: linux [00:43:46] Enabling bundled linux tools. [00:43:46] Found bwa - /usr/local/bin/bwa [00:43:46] Found bcftools - /usr/local/bin/bcftools [00:43:46] Found samtools - /usr/local/bin/samtools [00:43:46] Found java - /usr/local/bin/java [00:43:47] Found snpEff - /usr/local/bin/snpEff [00:43:47] Found samclip - /usr/local/bin/samclip [00:43:47] Found seqtk - /usr/local/bin/seqtk [00:43:47] Found parallel - /usr/local/bin/parallel [00:43:47] Found freebayes - /usr/local/bin/freebayes [00:43:47] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:43:47] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:43:47] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:43:47] Found vcfuniq - /usr/local/bin/vcfuniq [00:43:47] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:43:47] Found gzip - /bin/gzip [00:43:47] Found vt - /usr/local/bin/vt [00:43:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:43:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:43:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:43:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:43:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:43:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:43:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:43:48] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:46:49] This is snippy 4.6.0
Show full stderr[00:46:49] This is snippy 4.6.0 [00:46:49] Written by Torsten Seemann [00:46:49] Obtained from https://github.com/tseemann/snippy [00:46:49] Detected operating system: linux [00:46:49] Enabling bundled linux tools. [00:46:49] Found bwa - /usr/local/bin/bwa [00:46:49] Found bcftools - /usr/local/bin/bcftools [00:46:49] Found samtools - /usr/local/bin/samtools [00:46:49] Found java - /usr/local/bin/java [00:46:49] Found snpEff - /usr/local/bin/snpEff [00:46:49] Found samclip - /usr/local/bin/samclip [00:46:49] Found seqtk - /usr/local/bin/seqtk [00:46:49] Found parallel - /usr/local/bin/parallel [00:46:49] Found freebayes - /usr/local/bin/freebayes [00:46:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:46:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:46:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:46:49] Found vcfuniq - /usr/local/bin/vcfuniq [00:46:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:46:49] Found gzip - /bin/gzip [00:46:49] Found vt - /usr/local/bin/vt [00:46:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:46:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:46:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:46:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:46:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:46:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:46:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:46:50] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:47:04] This is snippy 4.6.0
Show full stderr[00:47:04] This is snippy 4.6.0 [00:47:04] Written by Torsten Seemann [00:47:04] Obtained from https://github.com/tseemann/snippy [00:47:04] Detected operating system: linux [00:47:04] Enabling bundled linux tools. [00:47:04] Found bwa - /usr/local/bin/bwa [00:47:04] Found bcftools - /usr/local/bin/bcftools [00:47:04] Found samtools - /usr/local/bin/samtools [00:47:04] Found java - /usr/local/bin/java [00:47:04] Found snpEff - /usr/local/bin/snpEff [00:47:04] Found samclip - /usr/local/bin/samclip [00:47:04] Found seqtk - /usr/local/bin/seqtk [00:47:04] Found parallel - /usr/local/bin/parallel [00:47:04] Found freebayes - /usr/local/bin/freebayes [00:47:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:47:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:47:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:47:04] Found vcfuniq - /usr/local/bin/vcfuniq [00:47:04] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:47:04] Found gzip - /bin/gzip [00:47:04] Found vt - /usr/local/bin/vt [00:47:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:47:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:47:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:47:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:47:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:47:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:47:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:47:05] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:17:33] This is snippy 4.6.0
Show full stderr[01:17:33] This is snippy 4.6.0 [01:17:33] Written by Torsten Seemann [01:17:33] Obtained from https://github.com/tseemann/snippy [01:17:33] Detected operating system: linux [01:17:33] Enabling bundled linux tools. [01:17:33] Found bwa - /usr/local/bin/bwa [01:17:33] Found bcftools - /usr/local/bin/bcftools [01:17:33] Found samtools - /usr/local/bin/samtools [01:17:33] Found java - /usr/local/bin/java [01:17:33] Found snpEff - /usr/local/bin/snpEff [01:17:33] Found samclip - /usr/local/bin/samclip [01:17:33] Found seqtk - /usr/local/bin/seqtk [01:17:33] Found parallel - /usr/local/bin/parallel [01:17:33] Found freebayes - /usr/local/bin/freebayes [01:17:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:17:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:17:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:17:33] Found vcfuniq - /usr/local/bin/vcfuniq [01:17:33] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:17:33] Found gzip - /bin/gzip [01:17:33] Found vt - /usr/local/bin/vt [01:17:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:17:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:17:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:17:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:17:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:17:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:17:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:17:34] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:47:16] This is snippy 4.6.0
Show full stderr[00:47:16] This is snippy 4.6.0 [00:47:16] Written by Torsten Seemann [00:47:16] Obtained from https://github.com/tseemann/snippy [00:47:16] Detected operating system: linux [00:47:16] Enabling bundled linux tools. [00:47:16] Found bwa - /usr/local/bin/bwa [00:47:16] Found bcftools - /usr/local/bin/bcftools [00:47:16] Found samtools - /usr/local/bin/samtools [00:47:16] Found java - /usr/local/bin/java [00:47:16] Found snpEff - /usr/local/bin/snpEff [00:47:16] Found samclip - /usr/local/bin/samclip [00:47:16] Found seqtk - /usr/local/bin/seqtk [00:47:16] Found parallel - /usr/local/bin/parallel [00:47:16] Found freebayes - /usr/local/bin/freebayes [00:47:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:47:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:47:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:47:16] Found vcfuniq - /usr/local/bin/vcfuniq [00:47:16] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:47:16] Found gzip - /bin/gzip [00:47:16] Found vt - /usr/local/bin/vt [00:47:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:47:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:47:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:47:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:47:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:47:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:47:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:47:17] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:17:51] This is snippy 4.6.0
Show full stderr[01:17:51] This is snippy 4.6.0 [01:17:51] Written by Torsten Seemann [01:17:51] Obtained from https://github.com/tseemann/snippy [01:17:51] Detected operating system: linux [01:17:51] Enabling bundled linux tools. [01:17:51] Found bwa - /usr/local/bin/bwa [01:17:51] Found bcftools - /usr/local/bin/bcftools [01:17:51] Found samtools - /usr/local/bin/samtools [01:17:51] Found java - /usr/local/bin/java [01:17:51] Found snpEff - /usr/local/bin/snpEff [01:17:51] Found samclip - /usr/local/bin/samclip [01:17:51] Found seqtk - /usr/local/bin/seqtk [01:17:51] Found parallel - /usr/local/bin/parallel [01:17:51] Found freebayes - /usr/local/bin/freebayes [01:17:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:17:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:17:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:17:51] Found vcfuniq - /usr/local/bin/vcfuniq [01:17:51] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:17:51] Found gzip - /bin/gzip [01:17:51] Found vt - /usr/local/bin/vt [01:17:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:17:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:17:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:17:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:17:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:17:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:17:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:17:52] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:25:03] This is snippy 4.6.0
Show full stderr[01:25:03] This is snippy 4.6.0 [01:25:03] Written by Torsten Seemann [01:25:03] Obtained from https://github.com/tseemann/snippy [01:25:03] Detected operating system: linux [01:25:03] Enabling bundled linux tools. [01:25:03] Found bwa - /usr/local/bin/bwa [01:25:03] Found bcftools - /usr/local/bin/bcftools [01:25:03] Found samtools - /usr/local/bin/samtools [01:25:03] Found java - /usr/local/bin/java [01:25:03] Found snpEff - /usr/local/bin/snpEff [01:25:03] Found samclip - /usr/local/bin/samclip [01:25:03] Found seqtk - /usr/local/bin/seqtk [01:25:03] Found parallel - /usr/local/bin/parallel [01:25:03] Found freebayes - /usr/local/bin/freebayes [01:25:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:25:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:25:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:25:03] Found vcfuniq - /usr/local/bin/vcfuniq [01:25:03] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:25:03] Found gzip - /bin/gzip [01:25:03] Found vt - /usr/local/bin/vt [01:25:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:25:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:25:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:25:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:25:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:25:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:25:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:25:04] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:59:48] This is snippy 4.6.0
Show full stderr[00:59:48] This is snippy 4.6.0 [00:59:48] Written by Torsten Seemann [00:59:48] Obtained from https://github.com/tseemann/snippy [00:59:48] Detected operating system: linux [00:59:48] Enabling bundled linux tools. [00:59:48] Found bwa - /usr/local/bin/bwa [00:59:48] Found bcftools - /usr/local/bin/bcftools [00:59:48] Found samtools - /usr/local/bin/samtools [00:59:48] Found java - /usr/local/bin/java [00:59:48] Found snpEff - /usr/local/bin/snpEff [00:59:48] Found samclip - /usr/local/bin/samclip [00:59:48] Found seqtk - /usr/local/bin/seqtk [00:59:48] Found parallel - /usr/local/bin/parallel [00:59:48] Found freebayes - /usr/local/bin/freebayes [00:59:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:59:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:59:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:59:48] Found vcfuniq - /usr/local/bin/vcfuniq [00:59:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:59:48] Found gzip - /bin/gzip [00:59:48] Found vt - /usr/local/bin/vt [00:59:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:59:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:59:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:59:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:59:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:59:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:59:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:59:49] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:00:06] This is snippy 4.6.0
Show full stderr[01:00:06] This is snippy 4.6.0 [01:00:06] Written by Torsten Seemann [01:00:06] Obtained from https://github.com/tseemann/snippy [01:00:06] Detected operating system: linux [01:00:06] Enabling bundled linux tools. [01:00:06] Found bwa - /usr/local/bin/bwa [01:00:06] Found bcftools - /usr/local/bin/bcftools [01:00:06] Found samtools - /usr/local/bin/samtools [01:00:06] Found java - /usr/local/bin/java [01:00:06] Found snpEff - /usr/local/bin/snpEff [01:00:06] Found samclip - /usr/local/bin/samclip [01:00:06] Found seqtk - /usr/local/bin/seqtk [01:00:06] Found parallel - /usr/local/bin/parallel [01:00:06] Found freebayes - /usr/local/bin/freebayes [01:00:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:00:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:00:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:00:06] Found vcfuniq - /usr/local/bin/vcfuniq [01:00:06] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:00:06] Found gzip - /bin/gzip [01:00:06] Found vt - /usr/local/bin/vt [01:00:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:00:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:00:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:00:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:00:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:00:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:00:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:00:07] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:37:48] This is snippy 4.6.0
Show full stderr[01:37:48] This is snippy 4.6.0 [01:37:48] Written by Torsten Seemann [01:37:48] Obtained from https://github.com/tseemann/snippy [01:37:48] Detected operating system: linux [01:37:48] Enabling bundled linux tools. [01:37:48] Found bwa - /usr/local/bin/bwa [01:37:48] Found bcftools - /usr/local/bin/bcftools [01:37:48] Found samtools - /usr/local/bin/samtools [01:37:48] Found java - /usr/local/bin/java [01:37:48] Found snpEff - /usr/local/bin/snpEff [01:37:48] Found samclip - /usr/local/bin/samclip [01:37:48] Found seqtk - /usr/local/bin/seqtk [01:37:48] Found parallel - /usr/local/bin/parallel [01:37:48] Found freebayes - /usr/local/bin/freebayes [01:37:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:37:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:37:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:37:48] Found vcfuniq - /usr/local/bin/vcfuniq [01:37:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:37:48] Found gzip - /bin/gzip [01:37:48] Found vt - /usr/local/bin/vt [01:37:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:37:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:37:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:37:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:37:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:37:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:37:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:37:48] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:37:51] This is snippy 4.6.0
Show full stderr[01:37:51] This is snippy 4.6.0 [01:37:51] Written by Torsten Seemann [01:37:51] Obtained from https://github.com/tseemann/snippy [01:37:51] Detected operating system: linux [01:37:51] Enabling bundled linux tools. [01:37:51] Found bwa - /usr/local/bin/bwa [01:37:51] Found bcftools - /usr/local/bin/bcftools [01:37:51] Found samtools - /usr/local/bin/samtools [01:37:51] Found java - /usr/local/bin/java [01:37:51] Found snpEff - /usr/local/bin/snpEff [01:37:51] Found samclip - /usr/local/bin/samclip [01:37:51] Found seqtk - /usr/local/bin/seqtk [01:37:51] Found parallel - /usr/local/bin/parallel [01:37:51] Found freebayes - /usr/local/bin/freebayes [01:37:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:37:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:37:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:37:51] Found vcfuniq - /usr/local/bin/vcfuniq [01:37:51] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:37:51] Found gzip - /bin/gzip [01:37:51] Found vt - /usr/local/bin/vt [01:37:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:37:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:37:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:37:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:37:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:37:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:37:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:37:52] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:44:01] This is snippy 4.6.0
Show full stderr[01:44:01] This is snippy 4.6.0 [01:44:01] Written by Torsten Seemann [01:44:01] Obtained from https://github.com/tseemann/snippy [01:44:01] Detected operating system: linux [01:44:01] Enabling bundled linux tools. [01:44:01] Found bwa - /usr/local/bin/bwa [01:44:01] Found bcftools - /usr/local/bin/bcftools [01:44:01] Found samtools - /usr/local/bin/samtools [01:44:01] Found java - /usr/local/bin/java [01:44:01] Found snpEff - /usr/local/bin/snpEff [01:44:01] Found samclip - /usr/local/bin/samclip [01:44:01] Found seqtk - /usr/local/bin/seqtk [01:44:01] Found parallel - /usr/local/bin/parallel [01:44:01] Found freebayes - /usr/local/bin/freebayes [01:44:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:44:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:44:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:44:01] Found vcfuniq - /usr/local/bin/vcfuniq [01:44:01] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:44:01] Found gzip - /bin/gzip [01:44:01] Found vt - /usr/local/bin/vt [01:44:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:44:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:44:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:44:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:44:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:44:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:44:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:44:03] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:05:13] This is snippy 4.6.0
Show full stderr[01:05:13] This is snippy 4.6.0 [01:05:13] Written by Torsten Seemann [01:05:13] Obtained from https://github.com/tseemann/snippy [01:05:13] Detected operating system: linux [01:05:13] Enabling bundled linux tools. [01:05:13] Found bwa - /usr/local/bin/bwa [01:05:13] Found bcftools - /usr/local/bin/bcftools [01:05:13] Found samtools - /usr/local/bin/samtools [01:05:13] Found java - /usr/local/bin/java [01:05:13] Found snpEff - /usr/local/bin/snpEff [01:05:13] Found samclip - /usr/local/bin/samclip [01:05:13] Found seqtk - /usr/local/bin/seqtk [01:05:13] Found parallel - /usr/local/bin/parallel [01:05:13] Found freebayes - /usr/local/bin/freebayes [01:05:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:05:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:05:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:05:13] Found vcfuniq - /usr/local/bin/vcfuniq [01:05:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:05:13] Found gzip - /bin/gzip [01:05:13] Found vt - /usr/local/bin/vt [01:05:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:05:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:05:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:05:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:05:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:05:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:05:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:05:14] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:05:48] This is snippy 4.6.0
Show full stderr[01:05:48] This is snippy 4.6.0 [01:05:48] Written by Torsten Seemann [01:05:48] Obtained from https://github.com/tseemann/snippy [01:05:48] Detected operating system: linux [01:05:48] Enabling bundled linux tools. [01:05:48] Found bwa - /usr/local/bin/bwa [01:05:48] Found bcftools - /usr/local/bin/bcftools [01:05:48] Found samtools - /usr/local/bin/samtools [01:05:48] Found java - /usr/local/bin/java [01:05:48] Found snpEff - /usr/local/bin/snpEff [01:05:48] Found samclip - /usr/local/bin/samclip [01:05:48] Found seqtk - /usr/local/bin/seqtk [01:05:48] Found parallel - /usr/local/bin/parallel [01:05:48] Found freebayes - /usr/local/bin/freebayes [01:05:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:05:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:05:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:05:48] Found vcfuniq - /usr/local/bin/vcfuniq [01:05:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:05:48] Found gzip - /bin/gzip [01:05:48] Found vt - /usr/local/bin/vt [01:05:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:05:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:05:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:05:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:05:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:05:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:05:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:05:49] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:45:57] This is snippy 4.6.0
Show full stderr[01:45:57] This is snippy 4.6.0 [01:45:57] Written by Torsten Seemann [01:45:57] Obtained from https://github.com/tseemann/snippy [01:45:57] Detected operating system: linux [01:45:57] Enabling bundled linux tools. [01:45:57] Found bwa - /usr/local/bin/bwa [01:45:57] Found bcftools - /usr/local/bin/bcftools [01:45:57] Found samtools - /usr/local/bin/samtools [01:45:57] Found java - /usr/local/bin/java [01:45:57] Found snpEff - /usr/local/bin/snpEff [01:45:57] Found samclip - /usr/local/bin/samclip [01:45:57] Found seqtk - /usr/local/bin/seqtk [01:45:57] Found parallel - /usr/local/bin/parallel [01:45:57] Found freebayes - /usr/local/bin/freebayes [01:45:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:45:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:45:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:45:57] Found vcfuniq - /usr/local/bin/vcfuniq [01:45:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:45:57] Found gzip - /bin/gzip [01:45:57] Found vt - /usr/local/bin/vt [01:45:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:45:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:45:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:45:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:45:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:45:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:45:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:45:58] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:09:16] This is snippy 4.6.0
Show full stderr[01:09:16] This is snippy 4.6.0 [01:09:16] Written by Torsten Seemann [01:09:16] Obtained from https://github.com/tseemann/snippy [01:09:16] Detected operating system: linux [01:09:16] Enabling bundled linux tools. [01:09:16] Found bwa - /usr/local/bin/bwa [01:09:16] Found bcftools - /usr/local/bin/bcftools [01:09:16] Found samtools - /usr/local/bin/samtools [01:09:16] Found java - /usr/local/bin/java [01:09:16] Found snpEff - /usr/local/bin/snpEff [01:09:16] Found samclip - /usr/local/bin/samclip [01:09:16] Found seqtk - /usr/local/bin/seqtk [01:09:16] Found parallel - /usr/local/bin/parallel [01:09:16] Found freebayes - /usr/local/bin/freebayes [01:09:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:09:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:09:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:09:16] Found vcfuniq - /usr/local/bin/vcfuniq [01:09:16] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:09:16] Found gzip - /bin/gzip [01:09:16] Found vt - /usr/local/bin/vt [01:09:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:09:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:09:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:09:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:09:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:09:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:09:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:09:17] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:33:08] This is snippy 4.6.0
Show full stderr[01:33:08] This is snippy 4.6.0 [01:33:08] Written by Torsten Seemann [01:33:08] Obtained from https://github.com/tseemann/snippy [01:33:08] Detected operating system: linux [01:33:08] Enabling bundled linux tools. [01:33:08] Found bwa - /usr/local/bin/bwa [01:33:08] Found bcftools - /usr/local/bin/bcftools [01:33:08] Found samtools - /usr/local/bin/samtools [01:33:08] Found java - /usr/local/bin/java [01:33:08] Found snpEff - /usr/local/bin/snpEff [01:33:08] Found samclip - /usr/local/bin/samclip [01:33:08] Found seqtk - /usr/local/bin/seqtk [01:33:08] Found parallel - /usr/local/bin/parallel [01:33:08] Found freebayes - /usr/local/bin/freebayes [01:33:08] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:33:08] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:33:08] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:33:08] Found vcfuniq - /usr/local/bin/vcfuniq [01:33:08] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:33:08] Found gzip - /bin/gzip [01:33:08] Found vt - /usr/local/bin/vt [01:33:08] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:33:08] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:33:08] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:33:08] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:33:08] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:33:09] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:33:09] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:33:09] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:23:15] This is snippy 4.6.0
Show full stderr[01:23:15] This is snippy 4.6.0 [01:23:15] Written by Torsten Seemann [01:23:15] Obtained from https://github.com/tseemann/snippy [01:23:15] Detected operating system: linux [01:23:15] Enabling bundled linux tools. [01:23:15] Found bwa - /usr/local/bin/bwa [01:23:15] Found bcftools - /usr/local/bin/bcftools [01:23:15] Found samtools - /usr/local/bin/samtools [01:23:15] Found java - /usr/local/bin/java [01:23:15] Found snpEff - /usr/local/bin/snpEff [01:23:15] Found samclip - /usr/local/bin/samclip [01:23:15] Found seqtk - /usr/local/bin/seqtk [01:23:15] Found parallel - /usr/local/bin/parallel [01:23:15] Found freebayes - /usr/local/bin/freebayes [01:23:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:23:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:23:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:23:15] Found vcfuniq - /usr/local/bin/vcfuniq [01:23:15] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:23:15] Found gzip - /bin/gzip [01:23:15] Found vt - /usr/local/bin/vt [01:23:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:23:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:23:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:23:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:23:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:23:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:23:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:23:16] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:23:42] This is snippy 4.6.0
Show full stderr[01:23:42] This is snippy 4.6.0 [01:23:42] Written by Torsten Seemann [01:23:42] Obtained from https://github.com/tseemann/snippy [01:23:42] Detected operating system: linux [01:23:42] Enabling bundled linux tools. [01:23:42] Found bwa - /usr/local/bin/bwa [01:23:42] Found bcftools - /usr/local/bin/bcftools [01:23:42] Found samtools - /usr/local/bin/samtools [01:23:42] Found java - /usr/local/bin/java [01:23:42] Found snpEff - /usr/local/bin/snpEff [01:23:42] Found samclip - /usr/local/bin/samclip [01:23:42] Found seqtk - /usr/local/bin/seqtk [01:23:42] Found parallel - /usr/local/bin/parallel [01:23:42] Found freebayes - /usr/local/bin/freebayes [01:23:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:23:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:23:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:23:42] Found vcfuniq - /usr/local/bin/vcfuniq [01:23:43] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:23:43] Found gzip - /bin/gzip [01:23:43] Found vt - /usr/local/bin/vt [01:23:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:23:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:23:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:23:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:23:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:23:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:23:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:23:43] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:24:18] This is snippy 4.6.0
Show full stderr[01:24:18] This is snippy 4.6.0 [01:24:18] Written by Torsten Seemann [01:24:18] Obtained from https://github.com/tseemann/snippy [01:24:18] Detected operating system: linux [01:24:18] Enabling bundled linux tools. [01:24:18] Found bwa - /usr/local/bin/bwa [01:24:18] Found bcftools - /usr/local/bin/bcftools [01:24:18] Found samtools - /usr/local/bin/samtools [01:24:18] Found java - /usr/local/bin/java [01:24:18] Found snpEff - /usr/local/bin/snpEff [01:24:18] Found samclip - /usr/local/bin/samclip [01:24:18] Found seqtk - /usr/local/bin/seqtk [01:24:18] Found parallel - /usr/local/bin/parallel [01:24:18] Found freebayes - /usr/local/bin/freebayes [01:24:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:24:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:24:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:24:18] Found vcfuniq - /usr/local/bin/vcfuniq [01:24:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:24:18] Found gzip - /bin/gzip [01:24:18] Found vt - /usr/local/bin/vt [01:24:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:24:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:24:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:24:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:24:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:24:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:24:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:24:19] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:24:45] This is snippy 4.6.0
Show full stderr[01:24:45] This is snippy 4.6.0 [01:24:45] Written by Torsten Seemann [01:24:45] Obtained from https://github.com/tseemann/snippy [01:24:45] Detected operating system: linux [01:24:45] Enabling bundled linux tools. [01:24:45] Found bwa - /usr/local/bin/bwa [01:24:45] Found bcftools - /usr/local/bin/bcftools [01:24:45] Found samtools - /usr/local/bin/samtools [01:24:45] Found java - /usr/local/bin/java [01:24:45] Found snpEff - /usr/local/bin/snpEff [01:24:45] Found samclip - /usr/local/bin/samclip [01:24:45] Found seqtk - /usr/local/bin/seqtk [01:24:45] Found parallel - /usr/local/bin/parallel [01:24:45] Found freebayes - /usr/local/bin/freebayes [01:24:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:24:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:24:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:24:45] Found vcfuniq - /usr/local/bin/vcfuniq [01:24:45] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:24:45] Found gzip - /bin/gzip [01:24:45] Found vt - /usr/local/bin/vt [01:24:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:24:46] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:24:46] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:24:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:24:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:24:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:24:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:24:46] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:36:49] This is snippy 4.6.0
Show full stderr[01:36:49] This is snippy 4.6.0 [01:36:49] Written by Torsten Seemann [01:36:49] Obtained from https://github.com/tseemann/snippy [01:36:49] Detected operating system: linux [01:36:49] Enabling bundled linux tools. [01:36:49] Found bwa - /usr/local/bin/bwa [01:36:49] Found bcftools - /usr/local/bin/bcftools [01:36:49] Found samtools - /usr/local/bin/samtools [01:36:49] Found java - /usr/local/bin/java [01:36:49] Found snpEff - /usr/local/bin/snpEff [01:36:49] Found samclip - /usr/local/bin/samclip [01:36:49] Found seqtk - /usr/local/bin/seqtk [01:36:49] Found parallel - /usr/local/bin/parallel [01:36:49] Found freebayes - /usr/local/bin/freebayes [01:36:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:36:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:36:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:36:49] Found vcfuniq - /usr/local/bin/vcfuniq [01:36:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:36:49] Found gzip - /bin/gzip [01:36:49] Found vt - /usr/local/bin/vt [01:36:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:36:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:36:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:36:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:36:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:36:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:36:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:36:50] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:24:57] This is snippy 4.6.0
Show full stderr[01:24:57] This is snippy 4.6.0 [01:24:57] Written by Torsten Seemann [01:24:57] Obtained from https://github.com/tseemann/snippy [01:24:57] Detected operating system: linux [01:24:57] Enabling bundled linux tools. [01:24:57] Found bwa - /usr/local/bin/bwa [01:24:57] Found bcftools - /usr/local/bin/bcftools [01:24:57] Found samtools - /usr/local/bin/samtools [01:24:57] Found java - /usr/local/bin/java [01:24:57] Found snpEff - /usr/local/bin/snpEff [01:24:57] Found samclip - /usr/local/bin/samclip [01:24:57] Found seqtk - /usr/local/bin/seqtk [01:24:57] Found parallel - /usr/local/bin/parallel [01:24:58] Found freebayes - /usr/local/bin/freebayes [01:24:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:24:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:24:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:24:58] Found vcfuniq - /usr/local/bin/vcfuniq [01:24:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:24:58] Found gzip - /bin/gzip [01:24:58] Found vt - /usr/local/bin/vt [01:24:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:24:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:24:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:24:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:24:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:24:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:24:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:24:58] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:39:13] This is snippy 4.6.0
Show full stderr[01:39:13] This is snippy 4.6.0 [01:39:13] Written by Torsten Seemann [01:39:13] Obtained from https://github.com/tseemann/snippy [01:39:13] Detected operating system: linux [01:39:13] Enabling bundled linux tools. [01:39:13] Found bwa - /usr/local/bin/bwa [01:39:13] Found bcftools - /usr/local/bin/bcftools [01:39:13] Found samtools - /usr/local/bin/samtools [01:39:13] Found java - /usr/local/bin/java [01:39:13] Found snpEff - /usr/local/bin/snpEff [01:39:13] Found samclip - /usr/local/bin/samclip [01:39:13] Found seqtk - /usr/local/bin/seqtk [01:39:13] Found parallel - /usr/local/bin/parallel [01:39:13] Found freebayes - /usr/local/bin/freebayes [01:39:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:39:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:39:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:39:13] Found vcfuniq - /usr/local/bin/vcfuniq [01:39:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:39:13] Found gzip - /bin/gzip [01:39:13] Found vt - /usr/local/bin/vt [01:39:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:39:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:39:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:39:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:39:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:39:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:39:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:39:17] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:25:01] This is snippy 4.6.0
Show full stderr[01:25:01] This is snippy 4.6.0 [01:25:01] Written by Torsten Seemann [01:25:01] Obtained from https://github.com/tseemann/snippy [01:25:01] Detected operating system: linux [01:25:01] Enabling bundled linux tools. [01:25:01] Found bwa - /usr/local/bin/bwa [01:25:01] Found bcftools - /usr/local/bin/bcftools [01:25:01] Found samtools - /usr/local/bin/samtools [01:25:01] Found java - /usr/local/bin/java [01:25:01] Found snpEff - /usr/local/bin/snpEff [01:25:01] Found samclip - /usr/local/bin/samclip [01:25:01] Found seqtk - /usr/local/bin/seqtk [01:25:01] Found parallel - /usr/local/bin/parallel [01:25:01] Found freebayes - /usr/local/bin/freebayes [01:25:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:25:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:25:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:25:01] Found vcfuniq - /usr/local/bin/vcfuniq [01:25:01] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:25:01] Found gzip - /bin/gzip [01:25:01] Found vt - /usr/local/bin/vt [01:25:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:25:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:25:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:25:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:25:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:25:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:25:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:25:02] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:25:07] This is snippy 4.6.0
Show full stderr[01:25:07] This is snippy 4.6.0 [01:25:07] Written by Torsten Seemann [01:25:07] Obtained from https://github.com/tseemann/snippy [01:25:07] Detected operating system: linux [01:25:07] Enabling bundled linux tools. [01:25:07] Found bwa - /usr/local/bin/bwa [01:25:07] Found bcftools - /usr/local/bin/bcftools [01:25:07] Found samtools - /usr/local/bin/samtools [01:25:07] Found java - /usr/local/bin/java [01:25:07] Found snpEff - /usr/local/bin/snpEff [01:25:07] Found samclip - /usr/local/bin/samclip [01:25:07] Found seqtk - /usr/local/bin/seqtk [01:25:07] Found parallel - /usr/local/bin/parallel [01:25:07] Found freebayes - /usr/local/bin/freebayes [01:25:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:25:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:25:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:25:07] Found vcfuniq - /usr/local/bin/vcfuniq [01:25:07] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:25:07] Found gzip - /bin/gzip [01:25:07] Found vt - /usr/local/bin/vt [01:25:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:25:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:25:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:25:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:25:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:25:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:25:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:25:08] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:25:12] This is snippy 4.6.0
Show full stderr[01:25:12] This is snippy 4.6.0 [01:25:12] Written by Torsten Seemann [01:25:12] Obtained from https://github.com/tseemann/snippy [01:25:12] Detected operating system: linux [01:25:12] Enabling bundled linux tools. [01:25:12] Found bwa - /usr/local/bin/bwa [01:25:12] Found bcftools - /usr/local/bin/bcftools [01:25:12] Found samtools - /usr/local/bin/samtools [01:25:12] Found java - /usr/local/bin/java [01:25:12] Found snpEff - /usr/local/bin/snpEff [01:25:12] Found samclip - /usr/local/bin/samclip [01:25:12] Found seqtk - /usr/local/bin/seqtk [01:25:12] Found parallel - /usr/local/bin/parallel [01:25:12] Found freebayes - /usr/local/bin/freebayes [01:25:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:25:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:25:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:25:12] Found vcfuniq - /usr/local/bin/vcfuniq [01:25:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:25:12] Found gzip - /bin/gzip [01:25:12] Found vt - /usr/local/bin/vt [01:25:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:25:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:25:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:25:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:25:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:25:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:25:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:25:13] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:25:30] This is snippy 4.6.0
Show full stderr[01:25:30] This is snippy 4.6.0 [01:25:30] Written by Torsten Seemann [01:25:30] Obtained from https://github.com/tseemann/snippy [01:25:30] Detected operating system: linux [01:25:30] Enabling bundled linux tools. [01:25:30] Found bwa - /usr/local/bin/bwa [01:25:30] Found bcftools - /usr/local/bin/bcftools [01:25:30] Found samtools - /usr/local/bin/samtools [01:25:30] Found java - /usr/local/bin/java [01:25:30] Found snpEff - /usr/local/bin/snpEff [01:25:30] Found samclip - /usr/local/bin/samclip [01:25:30] Found seqtk - /usr/local/bin/seqtk [01:25:30] Found parallel - /usr/local/bin/parallel [01:25:30] Found freebayes - /usr/local/bin/freebayes [01:25:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:25:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:25:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:25:30] Found vcfuniq - /usr/local/bin/vcfuniq [01:25:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:25:30] Found gzip - /bin/gzip [01:25:30] Found vt - /usr/local/bin/vt [01:25:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:25:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:25:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:25:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:25:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:25:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:25:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:25:31] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:25:28] This is snippy 4.6.0
Show full stderr[01:25:28] This is snippy 4.6.0 [01:25:28] Written by Torsten Seemann [01:25:28] Obtained from https://github.com/tseemann/snippy [01:25:28] Detected operating system: linux [01:25:28] Enabling bundled linux tools. [01:25:28] Found bwa - /usr/local/bin/bwa [01:25:28] Found bcftools - /usr/local/bin/bcftools [01:25:28] Found samtools - /usr/local/bin/samtools [01:25:28] Found java - /usr/local/bin/java [01:25:28] Found snpEff - /usr/local/bin/snpEff [01:25:28] Found samclip - /usr/local/bin/samclip [01:25:28] Found seqtk - /usr/local/bin/seqtk [01:25:28] Found parallel - /usr/local/bin/parallel [01:25:28] Found freebayes - /usr/local/bin/freebayes [01:25:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:25:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:25:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:25:28] Found vcfuniq - /usr/local/bin/vcfuniq [01:25:28] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:25:28] Found gzip - /bin/gzip [01:25:28] Found vt - /usr/local/bin/vt [01:25:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:25:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:25:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:25:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:25:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:25:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:25:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:25:29] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:45:18] This is snippy 4.6.0
Show full stderr[01:45:18] This is snippy 4.6.0 [01:45:18] Written by Torsten Seemann [01:45:18] Obtained from https://github.com/tseemann/snippy [01:45:18] Detected operating system: linux [01:45:18] Enabling bundled linux tools. [01:45:18] Found bwa - /usr/local/bin/bwa [01:45:18] Found bcftools - /usr/local/bin/bcftools [01:45:18] Found samtools - /usr/local/bin/samtools [01:45:18] Found java - /usr/local/bin/java [01:45:18] Found snpEff - /usr/local/bin/snpEff [01:45:18] Found samclip - /usr/local/bin/samclip [01:45:18] Found seqtk - /usr/local/bin/seqtk [01:45:18] Found parallel - /usr/local/bin/parallel [01:45:18] Found freebayes - /usr/local/bin/freebayes [01:45:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:45:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:45:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:45:18] Found vcfuniq - /usr/local/bin/vcfuniq [01:45:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:45:18] Found gzip - /bin/gzip [01:45:18] Found vt - /usr/local/bin/vt [01:45:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:45:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:45:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:45:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:45:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:45:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:45:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:45:19] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:25:48] This is snippy 4.6.0
Show full stderr[01:25:48] This is snippy 4.6.0 [01:25:48] Written by Torsten Seemann [01:25:48] Obtained from https://github.com/tseemann/snippy [01:25:48] Detected operating system: linux [01:25:48] Enabling bundled linux tools. [01:25:48] Found bwa - /usr/local/bin/bwa [01:25:48] Found bcftools - /usr/local/bin/bcftools [01:25:48] Found samtools - /usr/local/bin/samtools [01:25:48] Found java - /usr/local/bin/java [01:25:48] Found snpEff - /usr/local/bin/snpEff [01:25:48] Found samclip - /usr/local/bin/samclip [01:25:48] Found seqtk - /usr/local/bin/seqtk [01:25:48] Found parallel - /usr/local/bin/parallel [01:25:48] Found freebayes - /usr/local/bin/freebayes [01:25:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:25:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:25:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:25:48] Found vcfuniq - /usr/local/bin/vcfuniq [01:25:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:25:48] Found gzip - /bin/gzip [01:25:48] Found vt - /usr/local/bin/vt [01:25:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:25:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:25:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:25:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:25:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:25:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:25:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:25:50] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:26:09] This is snippy 4.6.0
Show full stderr[01:26:09] This is snippy 4.6.0 [01:26:09] Written by Torsten Seemann [01:26:09] Obtained from https://github.com/tseemann/snippy [01:26:09] Detected operating system: linux [01:26:09] Enabling bundled linux tools. [01:26:09] Found bwa - /usr/local/bin/bwa [01:26:09] Found bcftools - /usr/local/bin/bcftools [01:26:09] Found samtools - /usr/local/bin/samtools [01:26:09] Found java - /usr/local/bin/java [01:26:09] Found snpEff - /usr/local/bin/snpEff [01:26:09] Found samclip - /usr/local/bin/samclip [01:26:09] Found seqtk - /usr/local/bin/seqtk [01:26:09] Found parallel - /usr/local/bin/parallel [01:26:09] Found freebayes - /usr/local/bin/freebayes [01:26:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:26:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:26:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:26:09] Found vcfuniq - /usr/local/bin/vcfuniq [01:26:09] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:26:09] Found gzip - /bin/gzip [01:26:09] Found vt - /usr/local/bin/vt [01:26:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:26:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:26:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:26:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:26:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:26:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:26:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:26:10] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:33:14] This is snippy 4.6.0
Show full stderr[00:33:14] This is snippy 4.6.0 [00:33:14] Written by Torsten Seemann [00:33:14] Obtained from https://github.com/tseemann/snippy [00:33:14] Detected operating system: linux [00:33:14] Enabling bundled linux tools. [00:33:14] Found bwa - /usr/local/bin/bwa [00:33:14] Found bcftools - /usr/local/bin/bcftools [00:33:14] Found samtools - /usr/local/bin/samtools [00:33:14] Found java - /usr/local/bin/java [00:33:14] Found snpEff - /usr/local/bin/snpEff [00:33:14] Found samclip - /usr/local/bin/samclip [00:33:14] Found seqtk - /usr/local/bin/seqtk [00:33:14] Found parallel - /usr/local/bin/parallel [00:33:14] Found freebayes - /usr/local/bin/freebayes [00:33:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:33:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:33:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:33:14] Found vcfuniq - /usr/local/bin/vcfuniq [00:33:14] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:33:14] Found gzip - /bin/gzip [00:33:14] Found vt - /usr/local/bin/vt [00:33:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:33:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:33:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:33:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:33:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:33:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:33:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:33:15] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:58:50] This is snippy 4.6.0
Show full stderr[00:58:50] This is snippy 4.6.0 [00:58:50] Written by Torsten Seemann [00:58:50] Obtained from https://github.com/tseemann/snippy [00:58:50] Detected operating system: linux [00:58:50] Enabling bundled linux tools. [00:58:50] Found bwa - /usr/local/bin/bwa [00:58:50] Found bcftools - /usr/local/bin/bcftools [00:58:50] Found samtools - /usr/local/bin/samtools [00:58:50] Found java - /usr/local/bin/java [00:58:50] Found snpEff - /usr/local/bin/snpEff [00:58:50] Found samclip - /usr/local/bin/samclip [00:58:50] Found seqtk - /usr/local/bin/seqtk [00:58:50] Found parallel - /usr/local/bin/parallel [00:58:50] Found freebayes - /usr/local/bin/freebayes [00:58:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:58:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:58:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:58:50] Found vcfuniq - /usr/local/bin/vcfuniq [00:58:50] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:58:50] Found gzip - /bin/gzip [00:58:50] Found vt - /usr/local/bin/vt [00:58:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:58:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:58:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:58:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:58:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:58:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:58:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:58:51] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:33:24] This is snippy 4.6.0
Show full stderr[00:33:24] This is snippy 4.6.0 [00:33:24] Written by Torsten Seemann [00:33:24] Obtained from https://github.com/tseemann/snippy [00:33:24] Detected operating system: linux [00:33:24] Enabling bundled linux tools. [00:33:24] Found bwa - /usr/local/bin/bwa [00:33:24] Found bcftools - /usr/local/bin/bcftools [00:33:24] Found samtools - /usr/local/bin/samtools [00:33:24] Found java - /usr/local/bin/java [00:33:24] Found snpEff - /usr/local/bin/snpEff [00:33:24] Found samclip - /usr/local/bin/samclip [00:33:24] Found seqtk - /usr/local/bin/seqtk [00:33:24] Found parallel - /usr/local/bin/parallel [00:33:24] Found freebayes - /usr/local/bin/freebayes [00:33:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:33:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:33:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:33:24] Found vcfuniq - /usr/local/bin/vcfuniq [00:33:24] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:33:24] Found gzip - /bin/gzip [00:33:24] Found vt - /usr/local/bin/vt [00:33:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:33:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:33:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:33:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:33:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:33:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:33:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:33:25] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:33:39] This is snippy 4.6.0
Show full stderr[00:33:39] This is snippy 4.6.0 [00:33:39] Written by Torsten Seemann [00:33:39] Obtained from https://github.com/tseemann/snippy [00:33:39] Detected operating system: linux [00:33:39] Enabling bundled linux tools. [00:33:39] Found bwa - /usr/local/bin/bwa [00:33:39] Found bcftools - /usr/local/bin/bcftools [00:33:39] Found samtools - /usr/local/bin/samtools [00:33:39] Found java - /usr/local/bin/java [00:33:39] Found snpEff - /usr/local/bin/snpEff [00:33:39] Found samclip - /usr/local/bin/samclip [00:33:39] Found seqtk - /usr/local/bin/seqtk [00:33:39] Found parallel - /usr/local/bin/parallel [00:33:39] Found freebayes - /usr/local/bin/freebayes [00:33:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:33:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:33:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:33:39] Found vcfuniq - /usr/local/bin/vcfuniq [00:33:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:33:39] Found gzip - /bin/gzip [00:33:39] Found vt - /usr/local/bin/vt [00:33:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:33:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:33:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:33:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:33:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:33:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:33:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:33:40] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:35:12] This is snippy 4.6.0
Show full stderr[00:35:12] This is snippy 4.6.0 [00:35:12] Written by Torsten Seemann [00:35:12] Obtained from https://github.com/tseemann/snippy [00:35:12] Detected operating system: linux [00:35:12] Enabling bundled linux tools. [00:35:12] Found bwa - /usr/local/bin/bwa [00:35:12] Found bcftools - /usr/local/bin/bcftools [00:35:12] Found samtools - /usr/local/bin/samtools [00:35:12] Found java - /usr/local/bin/java [00:35:12] Found snpEff - /usr/local/bin/snpEff [00:35:12] Found samclip - /usr/local/bin/samclip [00:35:12] Found seqtk - /usr/local/bin/seqtk [00:35:12] Found parallel - /usr/local/bin/parallel [00:35:13] Found freebayes - /usr/local/bin/freebayes [00:35:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:35:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:35:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:35:13] Found vcfuniq - /usr/local/bin/vcfuniq [00:35:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:35:13] Found gzip - /bin/gzip [00:35:13] Found vt - /usr/local/bin/vt [00:35:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:35:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:35:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:35:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:35:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:35:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:35:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:35:18] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:35:26] This is snippy 4.6.0
Show full stderr[00:35:26] This is snippy 4.6.0 [00:35:26] Written by Torsten Seemann [00:35:26] Obtained from https://github.com/tseemann/snippy [00:35:26] Detected operating system: linux [00:35:26] Enabling bundled linux tools. [00:35:26] Found bwa - /usr/local/bin/bwa [00:35:26] Found bcftools - /usr/local/bin/bcftools [00:35:26] Found samtools - /usr/local/bin/samtools [00:35:26] Found java - /usr/local/bin/java [00:35:26] Found snpEff - /usr/local/bin/snpEff [00:35:26] Found samclip - /usr/local/bin/samclip [00:35:26] Found seqtk - /usr/local/bin/seqtk [00:35:26] Found parallel - /usr/local/bin/parallel [00:35:26] Found freebayes - /usr/local/bin/freebayes [00:35:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:35:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:35:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:35:26] Found vcfuniq - /usr/local/bin/vcfuniq [00:35:26] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:35:26] Found gzip - /bin/gzip [00:35:26] Found vt - /usr/local/bin/vt [00:35:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:35:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:35:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:35:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:35:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:35:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:35:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:35:27] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:33:53] This is snippy 4.6.0
Show full stderr[00:33:53] This is snippy 4.6.0 [00:33:53] Written by Torsten Seemann [00:33:53] Obtained from https://github.com/tseemann/snippy [00:33:53] Detected operating system: linux [00:33:53] Enabling bundled linux tools. [00:33:53] Found bwa - /usr/local/bin/bwa [00:33:53] Found bcftools - /usr/local/bin/bcftools [00:33:53] Found samtools - /usr/local/bin/samtools [00:33:53] Found java - /usr/local/bin/java [00:33:53] Found snpEff - /usr/local/bin/snpEff [00:33:53] Found samclip - /usr/local/bin/samclip [00:33:53] Found seqtk - /usr/local/bin/seqtk [00:33:53] Found parallel - /usr/local/bin/parallel [00:33:53] Found freebayes - /usr/local/bin/freebayes [00:33:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:33:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:33:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:33:53] Found vcfuniq - /usr/local/bin/vcfuniq [00:33:53] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:33:53] Found gzip - /bin/gzip [00:33:53] Found vt - /usr/local/bin/vt [00:33:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:33:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:33:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:33:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:33:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:33:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:33:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:33:54] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:33:57] This is snippy 4.6.0
Show full stderr[00:33:57] This is snippy 4.6.0 [00:33:57] Written by Torsten Seemann [00:33:57] Obtained from https://github.com/tseemann/snippy [00:33:57] Detected operating system: linux [00:33:57] Enabling bundled linux tools. [00:33:57] Found bwa - /usr/local/bin/bwa [00:33:57] Found bcftools - /usr/local/bin/bcftools [00:33:57] Found samtools - /usr/local/bin/samtools [00:33:57] Found java - /usr/local/bin/java [00:33:57] Found snpEff - /usr/local/bin/snpEff [00:33:57] Found samclip - /usr/local/bin/samclip [00:33:57] Found seqtk - /usr/local/bin/seqtk [00:33:57] Found parallel - /usr/local/bin/parallel [00:33:57] Found freebayes - /usr/local/bin/freebayes [00:33:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:33:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:33:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:33:57] Found vcfuniq - /usr/local/bin/vcfuniq [00:33:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:33:57] Found gzip - /bin/gzip [00:33:57] Found vt - /usr/local/bin/vt [00:33:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:33:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:33:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:33:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:33:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:33:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:33:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:33:58] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:35:55] This is snippy 4.6.0
Show full stderr[00:35:55] This is snippy 4.6.0 [00:35:55] Written by Torsten Seemann [00:35:55] Obtained from https://github.com/tseemann/snippy [00:35:55] Detected operating system: linux [00:35:55] Enabling bundled linux tools. [00:35:55] Found bwa - /usr/local/bin/bwa [00:35:55] Found bcftools - /usr/local/bin/bcftools [00:35:55] Found samtools - /usr/local/bin/samtools [00:35:55] Found java - /usr/local/bin/java [00:35:55] Found snpEff - /usr/local/bin/snpEff [00:35:55] Found samclip - /usr/local/bin/samclip [00:35:55] Found seqtk - /usr/local/bin/seqtk [00:35:55] Found parallel - /usr/local/bin/parallel [00:35:55] Found freebayes - /usr/local/bin/freebayes [00:35:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:35:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:35:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:35:55] Found vcfuniq - /usr/local/bin/vcfuniq [00:35:55] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:35:55] Found gzip - /bin/gzip [00:35:55] Found vt - /usr/local/bin/vt [00:35:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:35:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:35:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:35:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:35:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:35:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:35:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:35:56] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:36:09] This is snippy 4.6.0
Show full stderr[00:36:09] This is snippy 4.6.0 [00:36:09] Written by Torsten Seemann [00:36:09] Obtained from https://github.com/tseemann/snippy [00:36:09] Detected operating system: linux [00:36:09] Enabling bundled linux tools. [00:36:09] Found bwa - /usr/local/bin/bwa [00:36:09] Found bcftools - /usr/local/bin/bcftools [00:36:09] Found samtools - /usr/local/bin/samtools [00:36:09] Found java - /usr/local/bin/java [00:36:09] Found snpEff - /usr/local/bin/snpEff [00:36:09] Found samclip - /usr/local/bin/samclip [00:36:09] Found seqtk - /usr/local/bin/seqtk [00:36:09] Found parallel - /usr/local/bin/parallel [00:36:09] Found freebayes - /usr/local/bin/freebayes [00:36:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:36:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:36:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:36:09] Found vcfuniq - /usr/local/bin/vcfuniq [00:36:09] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:36:09] Found gzip - /bin/gzip [00:36:09] Found vt - /usr/local/bin/vt [00:36:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:36:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:36:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:36:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:36:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:36:09] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:36:09] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:36:09] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:41:47] This is snippy 4.6.0
Show full stderr[00:41:47] This is snippy 4.6.0 [00:41:47] Written by Torsten Seemann [00:41:47] Obtained from https://github.com/tseemann/snippy [00:41:47] Detected operating system: linux [00:41:47] Enabling bundled linux tools. [00:41:47] Found bwa - /usr/local/bin/bwa [00:41:47] Found bcftools - /usr/local/bin/bcftools [00:41:47] Found samtools - /usr/local/bin/samtools [00:41:47] Found java - /usr/local/bin/java [00:41:47] Found snpEff - /usr/local/bin/snpEff [00:41:48] Found samclip - /usr/local/bin/samclip [00:41:48] Found seqtk - /usr/local/bin/seqtk [00:41:48] Found parallel - /usr/local/bin/parallel [00:41:48] Found freebayes - /usr/local/bin/freebayes [00:41:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:41:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:41:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:41:48] Found vcfuniq - /usr/local/bin/vcfuniq [00:41:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:41:48] Found gzip - /bin/gzip [00:41:48] Found vt - /usr/local/bin/vt [00:41:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:41:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:41:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:41:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:41:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:41:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:41:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:41:49] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:34:09] This is snippy 4.6.0
Show full stderr[00:34:09] This is snippy 4.6.0 [00:34:09] Written by Torsten Seemann [00:34:09] Obtained from https://github.com/tseemann/snippy [00:34:09] Detected operating system: linux [00:34:09] Enabling bundled linux tools. [00:34:09] Found bwa - /usr/local/bin/bwa [00:34:09] Found bcftools - /usr/local/bin/bcftools [00:34:09] Found samtools - /usr/local/bin/samtools [00:34:09] Found java - /usr/local/bin/java [00:34:09] Found snpEff - /usr/local/bin/snpEff [00:34:09] Found samclip - /usr/local/bin/samclip [00:34:09] Found seqtk - /usr/local/bin/seqtk [00:34:09] Found parallel - /usr/local/bin/parallel [00:34:09] Found freebayes - /usr/local/bin/freebayes [00:34:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:34:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:34:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:34:09] Found vcfuniq - /usr/local/bin/vcfuniq [00:34:09] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:34:09] Found gzip - /bin/gzip [00:34:09] Found vt - /usr/local/bin/vt [00:34:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:34:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:34:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:34:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:34:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:34:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:34:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:34:10] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:34:12] This is snippy 4.6.0
Show full stderr[00:34:12] This is snippy 4.6.0 [00:34:12] Written by Torsten Seemann [00:34:12] Obtained from https://github.com/tseemann/snippy [00:34:12] Detected operating system: linux [00:34:12] Enabling bundled linux tools. [00:34:12] Found bwa - /usr/local/bin/bwa [00:34:12] Found bcftools - /usr/local/bin/bcftools [00:34:12] Found samtools - /usr/local/bin/samtools [00:34:12] Found java - /usr/local/bin/java [00:34:12] Found snpEff - /usr/local/bin/snpEff [00:34:12] Found samclip - /usr/local/bin/samclip [00:34:12] Found seqtk - /usr/local/bin/seqtk [00:34:12] Found parallel - /usr/local/bin/parallel [00:34:12] Found freebayes - /usr/local/bin/freebayes [00:34:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:34:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:34:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:34:12] Found vcfuniq - /usr/local/bin/vcfuniq [00:34:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:34:12] Found gzip - /bin/gzip [00:34:12] Found vt - /usr/local/bin/vt [00:34:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:34:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:34:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:34:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:34:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:34:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:34:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:34:13] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:53:44] This is snippy 4.6.0
Show full stderr[00:53:44] This is snippy 4.6.0 [00:53:44] Written by Torsten Seemann [00:53:44] Obtained from https://github.com/tseemann/snippy [00:53:44] Detected operating system: linux [00:53:44] Enabling bundled linux tools. [00:53:44] Found bwa - /usr/local/bin/bwa [00:53:44] Found bcftools - /usr/local/bin/bcftools [00:53:44] Found samtools - /usr/local/bin/samtools [00:53:44] Found java - /usr/local/bin/java [00:53:44] Found snpEff - /usr/local/bin/snpEff [00:53:44] Found samclip - /usr/local/bin/samclip [00:53:44] Found seqtk - /usr/local/bin/seqtk [00:53:44] Found parallel - /usr/local/bin/parallel [00:53:44] Found freebayes - /usr/local/bin/freebayes [00:53:44] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:53:44] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:53:44] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:53:44] Found vcfuniq - /usr/local/bin/vcfuniq [00:53:44] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:53:44] Found gzip - /bin/gzip [00:53:44] Found vt - /usr/local/bin/vt [00:53:44] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:53:44] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:53:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:53:45] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:53:45] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:53:45] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:53:45] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:53:45] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:26:21] This is snippy 4.6.0
Show full stderr[01:26:21] This is snippy 4.6.0 [01:26:21] Written by Torsten Seemann [01:26:21] Obtained from https://github.com/tseemann/snippy [01:26:21] Detected operating system: linux [01:26:21] Enabling bundled linux tools. [01:26:21] Found bwa - /usr/local/bin/bwa [01:26:21] Found bcftools - /usr/local/bin/bcftools [01:26:21] Found samtools - /usr/local/bin/samtools [01:26:21] Found java - /usr/local/bin/java [01:26:21] Found snpEff - /usr/local/bin/snpEff [01:26:21] Found samclip - /usr/local/bin/samclip [01:26:21] Found seqtk - /usr/local/bin/seqtk [01:26:21] Found parallel - /usr/local/bin/parallel [01:26:21] Found freebayes - /usr/local/bin/freebayes [01:26:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:26:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:26:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:26:21] Found vcfuniq - /usr/local/bin/vcfuniq [01:26:21] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:26:21] Found gzip - /bin/gzip [01:26:21] Found vt - /usr/local/bin/vt [01:26:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:26:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:26:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:26:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:26:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:26:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:26:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:26:21] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:29:37] This is snippy 4.6.0
Show full stderr[01:29:37] This is snippy 4.6.0 [01:29:37] Written by Torsten Seemann [01:29:37] Obtained from https://github.com/tseemann/snippy [01:29:37] Detected operating system: linux [01:29:37] Enabling bundled linux tools. [01:29:37] Found bwa - /usr/local/bin/bwa [01:29:37] Found bcftools - /usr/local/bin/bcftools [01:29:37] Found samtools - /usr/local/bin/samtools [01:29:37] Found java - /usr/local/bin/java [01:29:37] Found snpEff - /usr/local/bin/snpEff [01:29:37] Found samclip - /usr/local/bin/samclip [01:29:37] Found seqtk - /usr/local/bin/seqtk [01:29:37] Found parallel - /usr/local/bin/parallel [01:29:37] Found freebayes - /usr/local/bin/freebayes [01:29:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:29:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:29:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:29:37] Found vcfuniq - /usr/local/bin/vcfuniq [01:29:37] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:29:37] Found gzip - /bin/gzip [01:29:37] Found vt - /usr/local/bin/vt [01:29:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:29:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:29:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:29:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:29:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:29:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:29:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:29:38] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:31:24] This is snippy 4.6.0
Show full stderr[01:31:24] This is snippy 4.6.0 [01:31:24] Written by Torsten Seemann [01:31:24] Obtained from https://github.com/tseemann/snippy [01:31:24] Detected operating system: linux [01:31:24] Enabling bundled linux tools. [01:31:24] Found bwa - /usr/local/bin/bwa [01:31:24] Found bcftools - /usr/local/bin/bcftools [01:31:24] Found samtools - /usr/local/bin/samtools [01:31:24] Found java - /usr/local/bin/java [01:31:24] Found snpEff - /usr/local/bin/snpEff [01:31:24] Found samclip - /usr/local/bin/samclip [01:31:24] Found seqtk - /usr/local/bin/seqtk [01:31:24] Found parallel - /usr/local/bin/parallel [01:31:24] Found freebayes - /usr/local/bin/freebayes [01:31:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:31:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:31:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:31:24] Found vcfuniq - /usr/local/bin/vcfuniq [01:31:24] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:31:24] Found gzip - /bin/gzip [01:31:24] Found vt - /usr/local/bin/vt [01:31:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:31:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:31:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:31:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:31:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:31:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:31:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:31:25] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:31:39] This is snippy 4.6.0
Show full stderr[01:31:39] This is snippy 4.6.0 [01:31:39] Written by Torsten Seemann [01:31:39] Obtained from https://github.com/tseemann/snippy [01:31:39] Detected operating system: linux [01:31:39] Enabling bundled linux tools. [01:31:39] Found bwa - /usr/local/bin/bwa [01:31:39] Found bcftools - /usr/local/bin/bcftools [01:31:39] Found samtools - /usr/local/bin/samtools [01:31:39] Found java - /usr/local/bin/java [01:31:39] Found snpEff - /usr/local/bin/snpEff [01:31:39] Found samclip - /usr/local/bin/samclip [01:31:39] Found seqtk - /usr/local/bin/seqtk [01:31:39] Found parallel - /usr/local/bin/parallel [01:31:39] Found freebayes - /usr/local/bin/freebayes [01:31:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:31:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:31:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:31:39] Found vcfuniq - /usr/local/bin/vcfuniq [01:31:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:31:39] Found gzip - /bin/gzip [01:31:39] Found vt - /usr/local/bin/vt [01:31:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:31:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:31:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:31:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:31:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:31:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:31:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:31:40] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:34:19] This is snippy 4.6.0
Show full stderr[01:34:19] This is snippy 4.6.0 [01:34:19] Written by Torsten Seemann [01:34:19] Obtained from https://github.com/tseemann/snippy [01:34:19] Detected operating system: linux [01:34:19] Enabling bundled linux tools. [01:34:19] Found bwa - /usr/local/bin/bwa [01:34:19] Found bcftools - /usr/local/bin/bcftools [01:34:19] Found samtools - /usr/local/bin/samtools [01:34:19] Found java - /usr/local/bin/java [01:34:19] Found snpEff - /usr/local/bin/snpEff [01:34:19] Found samclip - /usr/local/bin/samclip [01:34:19] Found seqtk - /usr/local/bin/seqtk [01:34:19] Found parallel - /usr/local/bin/parallel [01:34:19] Found freebayes - /usr/local/bin/freebayes [01:34:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:34:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:34:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:34:19] Found vcfuniq - /usr/local/bin/vcfuniq [01:34:19] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:34:19] Found gzip - /bin/gzip [01:34:19] Found vt - /usr/local/bin/vt [01:34:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:34:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:34:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:34:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:34:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:34:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:34:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:34:20] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:36:34] This is snippy 4.6.0
Show full stderr[01:36:34] This is snippy 4.6.0 [01:36:34] Written by Torsten Seemann [01:36:34] Obtained from https://github.com/tseemann/snippy [01:36:34] Detected operating system: linux [01:36:34] Enabling bundled linux tools. [01:36:34] Found bwa - /usr/local/bin/bwa [01:36:34] Found bcftools - /usr/local/bin/bcftools [01:36:34] Found samtools - /usr/local/bin/samtools [01:36:34] Found java - /usr/local/bin/java [01:36:34] Found snpEff - /usr/local/bin/snpEff [01:36:34] Found samclip - /usr/local/bin/samclip [01:36:34] Found seqtk - /usr/local/bin/seqtk [01:36:35] Found parallel - /usr/local/bin/parallel [01:36:35] Found freebayes - /usr/local/bin/freebayes [01:36:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:36:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:36:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:36:35] Found vcfuniq - /usr/local/bin/vcfuniq [01:36:35] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:36:35] Found gzip - /bin/gzip [01:36:35] Found vt - /usr/local/bin/vt [01:36:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:36:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:36:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:36:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:36:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:36:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:36:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:36:37] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:50:07] This is snippy 4.6.0
Show full stderr[01:50:07] This is snippy 4.6.0 [01:50:07] Written by Torsten Seemann [01:50:07] Obtained from https://github.com/tseemann/snippy [01:50:07] Detected operating system: linux [01:50:07] Enabling bundled linux tools. [01:50:07] Found bwa - /usr/local/bin/bwa [01:50:07] Found bcftools - /usr/local/bin/bcftools [01:50:07] Found samtools - /usr/local/bin/samtools [01:50:07] Found java - /usr/local/bin/java [01:50:07] Found snpEff - /usr/local/bin/snpEff [01:50:07] Found samclip - /usr/local/bin/samclip [01:50:07] Found seqtk - /usr/local/bin/seqtk [01:50:07] Found parallel - /usr/local/bin/parallel [01:50:07] Found freebayes - /usr/local/bin/freebayes [01:50:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:50:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:50:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:50:07] Found vcfuniq - /usr/local/bin/vcfuniq [01:50:07] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:50:07] Found gzip - /bin/gzip [01:50:07] Found vt - /usr/local/bin/vt [01:50:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:50:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:50:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:50:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:50:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:50:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:50:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:50:07] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:57:58] This is snippy 4.6.0
Show full stderr[01:57:58] This is snippy 4.6.0 [01:57:58] Written by Torsten Seemann [01:57:58] Obtained from https://github.com/tseemann/snippy [01:57:58] Detected operating system: linux [01:57:58] Enabling bundled linux tools. [01:57:58] Found bwa - /usr/local/bin/bwa [01:57:58] Found bcftools - /usr/local/bin/bcftools [01:57:58] Found samtools - /usr/local/bin/samtools [01:57:58] Found java - /usr/local/bin/java [01:57:58] Found snpEff - /usr/local/bin/snpEff [01:57:58] Found samclip - /usr/local/bin/samclip [01:57:58] Found seqtk - /usr/local/bin/seqtk [01:57:58] Found parallel - /usr/local/bin/parallel [01:57:58] Found freebayes - /usr/local/bin/freebayes [01:57:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:57:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:57:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:57:58] Found vcfuniq - /usr/local/bin/vcfuniq [01:57:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:57:58] Found gzip - /bin/gzip [01:57:58] Found vt - /usr/local/bin/vt [01:57:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:57:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:57:59] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:57:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:57:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:58:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:58:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:58:01] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:45:38] This is snippy 4.6.0
Show full stderr[01:45:38] This is snippy 4.6.0 [01:45:38] Written by Torsten Seemann [01:45:38] Obtained from https://github.com/tseemann/snippy [01:45:38] Detected operating system: linux [01:45:38] Enabling bundled linux tools. [01:45:38] Found bwa - /usr/local/bin/bwa [01:45:38] Found bcftools - /usr/local/bin/bcftools [01:45:38] Found samtools - /usr/local/bin/samtools [01:45:38] Found java - /usr/local/bin/java [01:45:38] Found snpEff - /usr/local/bin/snpEff [01:45:38] Found samclip - /usr/local/bin/samclip [01:45:38] Found seqtk - /usr/local/bin/seqtk [01:45:38] Found parallel - /usr/local/bin/parallel [01:45:38] Found freebayes - /usr/local/bin/freebayes [01:45:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:45:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:45:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:45:38] Found vcfuniq - /usr/local/bin/vcfuniq [01:45:38] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:45:38] Found gzip - /bin/gzip [01:45:38] Found vt - /usr/local/bin/vt [01:45:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:45:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:45:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:45:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:45:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:45:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:45:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:45:39] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:46:15] This is snippy 4.6.0
Show full stderr[01:46:15] This is snippy 4.6.0 [01:46:15] Written by Torsten Seemann [01:46:15] Obtained from https://github.com/tseemann/snippy [01:46:15] Detected operating system: linux [01:46:15] Enabling bundled linux tools. [01:46:15] Found bwa - /usr/local/bin/bwa [01:46:15] Found bcftools - /usr/local/bin/bcftools [01:46:15] Found samtools - /usr/local/bin/samtools [01:46:15] Found java - /usr/local/bin/java [01:46:15] Found snpEff - /usr/local/bin/snpEff [01:46:15] Found samclip - /usr/local/bin/samclip [01:46:15] Found seqtk - /usr/local/bin/seqtk [01:46:15] Found parallel - /usr/local/bin/parallel [01:46:15] Found freebayes - /usr/local/bin/freebayes [01:46:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:46:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:46:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:46:15] Found vcfuniq - /usr/local/bin/vcfuniq [01:46:15] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:46:15] Found gzip - /bin/gzip [01:46:15] Found vt - /usr/local/bin/vt [01:46:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:46:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:46:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:46:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:46:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:46:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:46:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:46:16] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:46:30] This is snippy 4.6.0
Show full stderr[01:46:30] This is snippy 4.6.0 [01:46:30] Written by Torsten Seemann [01:46:30] Obtained from https://github.com/tseemann/snippy [01:46:30] Detected operating system: linux [01:46:30] Enabling bundled linux tools. [01:46:30] Found bwa - /usr/local/bin/bwa [01:46:30] Found bcftools - /usr/local/bin/bcftools [01:46:30] Found samtools - /usr/local/bin/samtools [01:46:30] Found java - /usr/local/bin/java [01:46:30] Found snpEff - /usr/local/bin/snpEff [01:46:30] Found samclip - /usr/local/bin/samclip [01:46:30] Found seqtk - /usr/local/bin/seqtk [01:46:30] Found parallel - /usr/local/bin/parallel [01:46:30] Found freebayes - /usr/local/bin/freebayes [01:46:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:46:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:46:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:46:30] Found vcfuniq - /usr/local/bin/vcfuniq [01:46:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:46:30] Found gzip - /bin/gzip [01:46:30] Found vt - /usr/local/bin/vt [01:46:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:46:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:46:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:46:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:46:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:46:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:46:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:46:31] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:47:42] This is snippy 4.6.0
Show full stderr[01:47:42] This is snippy 4.6.0 [01:47:42] Written by Torsten Seemann [01:47:42] Obtained from https://github.com/tseemann/snippy [01:47:42] Detected operating system: linux [01:47:42] Enabling bundled linux tools. [01:47:42] Found bwa - /usr/local/bin/bwa [01:47:42] Found bcftools - /usr/local/bin/bcftools [01:47:42] Found samtools - /usr/local/bin/samtools [01:47:42] Found java - /usr/local/bin/java [01:47:42] Found snpEff - /usr/local/bin/snpEff [01:47:42] Found samclip - /usr/local/bin/samclip [01:47:42] Found seqtk - /usr/local/bin/seqtk [01:47:42] Found parallel - /usr/local/bin/parallel [01:47:42] Found freebayes - /usr/local/bin/freebayes [01:47:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:47:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:47:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:47:42] Found vcfuniq - /usr/local/bin/vcfuniq [01:47:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:47:42] Found gzip - /bin/gzip [01:47:42] Found vt - /usr/local/bin/vt [01:47:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:47:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:47:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:47:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:47:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:47:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:47:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:47:43] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:47:54] This is snippy 4.6.0
Show full stderr[01:47:54] This is snippy 4.6.0 [01:47:54] Written by Torsten Seemann [01:47:54] Obtained from https://github.com/tseemann/snippy [01:47:54] Detected operating system: linux [01:47:54] Enabling bundled linux tools. [01:47:54] Found bwa - /usr/local/bin/bwa [01:47:54] Found bcftools - /usr/local/bin/bcftools [01:47:54] Found samtools - /usr/local/bin/samtools [01:47:54] Found java - /usr/local/bin/java [01:47:54] Found snpEff - /usr/local/bin/snpEff [01:47:54] Found samclip - /usr/local/bin/samclip [01:47:54] Found seqtk - /usr/local/bin/seqtk [01:47:54] Found parallel - /usr/local/bin/parallel [01:47:54] Found freebayes - /usr/local/bin/freebayes [01:47:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:47:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:47:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:47:54] Found vcfuniq - /usr/local/bin/vcfuniq [01:47:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:47:54] Found gzip - /bin/gzip [01:47:54] Found vt - /usr/local/bin/vt [01:47:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:47:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:47:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:47:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:47:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:47:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:47:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:47:55] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:59:41] This is snippy 4.6.0
Show full stderr[01:59:41] This is snippy 4.6.0 [01:59:41] Written by Torsten Seemann [01:59:41] Obtained from https://github.com/tseemann/snippy [01:59:41] Detected operating system: linux [01:59:41] Enabling bundled linux tools. [01:59:41] Found bwa - /usr/local/bin/bwa [01:59:42] Found bcftools - /usr/local/bin/bcftools [01:59:42] Found samtools - /usr/local/bin/samtools [01:59:42] Found java - /usr/local/bin/java [01:59:42] Found snpEff - /usr/local/bin/snpEff [01:59:42] Found samclip - /usr/local/bin/samclip [01:59:42] Found seqtk - /usr/local/bin/seqtk [01:59:42] Found parallel - /usr/local/bin/parallel [01:59:42] Found freebayes - /usr/local/bin/freebayes [01:59:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:59:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:59:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:59:42] Found vcfuniq - /usr/local/bin/vcfuniq [01:59:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:59:42] Found gzip - /bin/gzip [01:59:42] Found vt - /usr/local/bin/vt [01:59:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:59:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:59:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:59:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:59:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:59:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:59:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:59:43] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:10:16] This is snippy 4.6.0
Show full stderr[01:10:16] This is snippy 4.6.0 [01:10:16] Written by Torsten Seemann [01:10:16] Obtained from https://github.com/tseemann/snippy [01:10:16] Detected operating system: linux [01:10:16] Enabling bundled linux tools. [01:10:16] Found bwa - /usr/local/bin/bwa [01:10:16] Found bcftools - /usr/local/bin/bcftools [01:10:16] Found samtools - /usr/local/bin/samtools [01:10:16] Found java - /usr/local/bin/java [01:10:16] Found snpEff - /usr/local/bin/snpEff [01:10:17] Found samclip - /usr/local/bin/samclip [01:10:17] Found seqtk - /usr/local/bin/seqtk [01:10:17] Found parallel - /usr/local/bin/parallel [01:10:17] Found freebayes - /usr/local/bin/freebayes [01:10:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:10:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:10:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:10:17] Found vcfuniq - /usr/local/bin/vcfuniq [01:10:17] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:10:17] Found gzip - /bin/gzip [01:10:17] Found vt - /usr/local/bin/vt [01:10:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:10:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:10:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:10:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:10:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:10:18] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:10:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:10:18] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:10:31] This is snippy 4.6.0
Show full stderr[01:10:31] This is snippy 4.6.0 [01:10:31] Written by Torsten Seemann [01:10:31] Obtained from https://github.com/tseemann/snippy [01:10:31] Detected operating system: linux [01:10:31] Enabling bundled linux tools. [01:10:31] Found bwa - /usr/local/bin/bwa [01:10:31] Found bcftools - /usr/local/bin/bcftools [01:10:31] Found samtools - /usr/local/bin/samtools [01:10:31] Found java - /usr/local/bin/java [01:10:31] Found snpEff - /usr/local/bin/snpEff [01:10:31] Found samclip - /usr/local/bin/samclip [01:10:31] Found seqtk - /usr/local/bin/seqtk [01:10:31] Found parallel - /usr/local/bin/parallel [01:10:31] Found freebayes - /usr/local/bin/freebayes [01:10:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:10:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:10:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:10:32] Found vcfuniq - /usr/local/bin/vcfuniq [01:10:32] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:10:32] Found gzip - /bin/gzip [01:10:32] Found vt - /usr/local/bin/vt [01:10:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:10:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:10:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:10:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:10:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:10:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:10:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:10:32] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:13:13] This is snippy 4.6.0
Show full stderr[01:13:13] This is snippy 4.6.0 [01:13:13] Written by Torsten Seemann [01:13:13] Obtained from https://github.com/tseemann/snippy [01:13:13] Detected operating system: linux [01:13:13] Enabling bundled linux tools. [01:13:13] Found bwa - /usr/local/bin/bwa [01:13:13] Found bcftools - /usr/local/bin/bcftools [01:13:13] Found samtools - /usr/local/bin/samtools [01:13:13] Found java - /usr/local/bin/java [01:13:13] Found snpEff - /usr/local/bin/snpEff [01:13:13] Found samclip - /usr/local/bin/samclip [01:13:13] Found seqtk - /usr/local/bin/seqtk [01:13:13] Found parallel - /usr/local/bin/parallel [01:13:13] Found freebayes - /usr/local/bin/freebayes [01:13:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:13:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:13:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:13:13] Found vcfuniq - /usr/local/bin/vcfuniq [01:13:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:13:13] Found gzip - /bin/gzip [01:13:13] Found vt - /usr/local/bin/vt [01:13:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:13:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:13:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:13:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:13:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:13:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:13:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:13:14] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:46:10] This is snippy 4.6.0
Show full stderr[01:46:10] This is snippy 4.6.0 [01:46:10] Written by Torsten Seemann [01:46:10] Obtained from https://github.com/tseemann/snippy [01:46:10] Detected operating system: linux [01:46:10] Enabling bundled linux tools. [01:46:10] Found bwa - /usr/local/bin/bwa [01:46:10] Found bcftools - /usr/local/bin/bcftools [01:46:10] Found samtools - /usr/local/bin/samtools [01:46:10] Found java - /usr/local/bin/java [01:46:10] Found snpEff - /usr/local/bin/snpEff [01:46:10] Found samclip - /usr/local/bin/samclip [01:46:10] Found seqtk - /usr/local/bin/seqtk [01:46:10] Found parallel - /usr/local/bin/parallel [01:46:10] Found freebayes - /usr/local/bin/freebayes [01:46:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:46:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:46:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:46:10] Found vcfuniq - /usr/local/bin/vcfuniq [01:46:10] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:46:10] Found gzip - /bin/gzip [01:46:10] Found vt - /usr/local/bin/vt [01:46:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:46:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:46:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:46:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:46:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:46:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:46:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:46:10] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:13:57] This is snippy 4.6.0
Show full stderr[01:13:57] This is snippy 4.6.0 [01:13:57] Written by Torsten Seemann [01:13:57] Obtained from https://github.com/tseemann/snippy [01:13:57] Detected operating system: linux [01:13:57] Enabling bundled linux tools. [01:13:57] Found bwa - /usr/local/bin/bwa [01:13:57] Found bcftools - /usr/local/bin/bcftools [01:13:57] Found samtools - /usr/local/bin/samtools [01:13:57] Found java - /usr/local/bin/java [01:13:57] Found snpEff - /usr/local/bin/snpEff [01:13:57] Found samclip - /usr/local/bin/samclip [01:13:57] Found seqtk - /usr/local/bin/seqtk [01:13:57] Found parallel - /usr/local/bin/parallel [01:13:57] Found freebayes - /usr/local/bin/freebayes [01:13:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:13:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:13:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:13:57] Found vcfuniq - /usr/local/bin/vcfuniq [01:13:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:13:57] Found gzip - /bin/gzip [01:13:57] Found vt - /usr/local/bin/vt [01:13:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:13:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:13:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:13:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:13:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:13:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:13:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:13:58] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:47:39] This is snippy 4.6.0
Show full stderr[01:47:39] This is snippy 4.6.0 [01:47:39] Written by Torsten Seemann [01:47:39] Obtained from https://github.com/tseemann/snippy [01:47:39] Detected operating system: linux [01:47:39] Enabling bundled linux tools. [01:47:39] Found bwa - /usr/local/bin/bwa [01:47:39] Found bcftools - /usr/local/bin/bcftools [01:47:39] Found samtools - /usr/local/bin/samtools [01:47:39] Found java - /usr/local/bin/java [01:47:39] Found snpEff - /usr/local/bin/snpEff [01:47:39] Found samclip - /usr/local/bin/samclip [01:47:39] Found seqtk - /usr/local/bin/seqtk [01:47:39] Found parallel - /usr/local/bin/parallel [01:47:39] Found freebayes - /usr/local/bin/freebayes [01:47:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:47:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:47:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:47:39] Found vcfuniq - /usr/local/bin/vcfuniq [01:47:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:47:39] Found gzip - /bin/gzip [01:47:39] Found vt - /usr/local/bin/vt [01:47:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:47:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:47:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:47:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:47:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:47:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:47:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:47:41] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:14:12] This is snippy 4.6.0
Show full stderr[01:14:12] This is snippy 4.6.0 [01:14:12] Written by Torsten Seemann [01:14:12] Obtained from https://github.com/tseemann/snippy [01:14:12] Detected operating system: linux [01:14:12] Enabling bundled linux tools. [01:14:12] Found bwa - /usr/local/bin/bwa [01:14:12] Found bcftools - /usr/local/bin/bcftools [01:14:12] Found samtools - /usr/local/bin/samtools [01:14:12] Found java - /usr/local/bin/java [01:14:12] Found snpEff - /usr/local/bin/snpEff [01:14:12] Found samclip - /usr/local/bin/samclip [01:14:12] Found seqtk - /usr/local/bin/seqtk [01:14:12] Found parallel - /usr/local/bin/parallel [01:14:12] Found freebayes - /usr/local/bin/freebayes [01:14:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:14:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:14:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:14:12] Found vcfuniq - /usr/local/bin/vcfuniq [01:14:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:14:12] Found gzip - /bin/gzip [01:14:12] Found vt - /usr/local/bin/vt [01:14:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:14:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:14:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:14:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:14:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:14:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:14:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:14:13] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:14:30] This is snippy 4.6.0
Show full stderr[01:14:30] This is snippy 4.6.0 [01:14:30] Written by Torsten Seemann [01:14:30] Obtained from https://github.com/tseemann/snippy [01:14:30] Detected operating system: linux [01:14:30] Enabling bundled linux tools. [01:14:30] Found bwa - /usr/local/bin/bwa [01:14:30] Found bcftools - /usr/local/bin/bcftools [01:14:30] Found samtools - /usr/local/bin/samtools [01:14:30] Found java - /usr/local/bin/java [01:14:30] Found snpEff - /usr/local/bin/snpEff [01:14:30] Found samclip - /usr/local/bin/samclip [01:14:30] Found seqtk - /usr/local/bin/seqtk [01:14:30] Found parallel - /usr/local/bin/parallel [01:14:30] Found freebayes - /usr/local/bin/freebayes [01:14:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:14:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:14:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:14:30] Found vcfuniq - /usr/local/bin/vcfuniq [01:14:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:14:30] Found gzip - /bin/gzip [01:14:30] Found vt - /usr/local/bin/vt [01:14:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:14:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:14:30] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:14:30] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:14:30] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:14:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:14:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:14:31] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:15:24] This is snippy 4.6.0
Show full stderr[01:15:24] This is snippy 4.6.0 [01:15:24] Written by Torsten Seemann [01:15:24] Obtained from https://github.com/tseemann/snippy [01:15:24] Detected operating system: linux [01:15:24] Enabling bundled linux tools. [01:15:24] Found bwa - /usr/local/bin/bwa [01:15:24] Found bcftools - /usr/local/bin/bcftools [01:15:24] Found samtools - /usr/local/bin/samtools [01:15:24] Found java - /usr/local/bin/java [01:15:24] Found snpEff - /usr/local/bin/snpEff [01:15:24] Found samclip - /usr/local/bin/samclip [01:15:24] Found seqtk - /usr/local/bin/seqtk [01:15:24] Found parallel - /usr/local/bin/parallel [01:15:24] Found freebayes - /usr/local/bin/freebayes [01:15:24] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:15:24] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:15:24] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:15:24] Found vcfuniq - /usr/local/bin/vcfuniq [01:15:24] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:15:24] Found gzip - /bin/gzip [01:15:24] Found vt - /usr/local/bin/vt [01:15:24] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:15:24] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:15:24] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:15:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:15:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:15:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:15:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:15:25] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:51:24] This is snippy 4.6.0
Show full stderr[01:51:24] This is snippy 4.6.0 [01:51:24] Written by Torsten Seemann [01:51:24] Obtained from https://github.com/tseemann/snippy [01:51:24] Detected operating system: linux [01:51:24] Enabling bundled linux tools. [01:51:24] Found bwa - /usr/local/bin/bwa [01:51:24] Found bcftools - /usr/local/bin/bcftools [01:51:24] Found samtools - /usr/local/bin/samtools [01:51:24] Found java - /usr/local/bin/java [01:51:24] Found snpEff - /usr/local/bin/snpEff [01:51:24] Found samclip - /usr/local/bin/samclip [01:51:24] Found seqtk - /usr/local/bin/seqtk [01:51:24] Found parallel - /usr/local/bin/parallel [01:51:25] Found freebayes - /usr/local/bin/freebayes [01:51:25] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:51:25] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:51:25] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:51:25] Found vcfuniq - /usr/local/bin/vcfuniq [01:51:25] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:51:25] Found gzip - /bin/gzip [01:51:25] Found vt - /usr/local/bin/vt [01:51:25] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:51:25] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:51:25] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:51:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:51:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:51:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:51:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:51:25] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:20:30] This is snippy 4.6.0
Show full stderr[01:20:30] This is snippy 4.6.0 [01:20:30] Written by Torsten Seemann [01:20:30] Obtained from https://github.com/tseemann/snippy [01:20:30] Detected operating system: linux [01:20:30] Enabling bundled linux tools. [01:20:30] Found bwa - /usr/local/bin/bwa [01:20:30] Found bcftools - /usr/local/bin/bcftools [01:20:30] Found samtools - /usr/local/bin/samtools [01:20:30] Found java - /usr/local/bin/java [01:20:30] Found snpEff - /usr/local/bin/snpEff [01:20:30] Found samclip - /usr/local/bin/samclip [01:20:30] Found seqtk - /usr/local/bin/seqtk [01:20:30] Found parallel - /usr/local/bin/parallel [01:20:30] Found freebayes - /usr/local/bin/freebayes [01:20:30] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:20:30] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:20:30] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:20:30] Found vcfuniq - /usr/local/bin/vcfuniq [01:20:30] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:20:30] Found gzip - /bin/gzip [01:20:30] Found vt - /usr/local/bin/vt [01:20:30] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:20:30] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:20:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:20:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:20:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:20:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:20:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:20:32] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:21:02] This is snippy 4.6.0
Show full stderr[01:21:02] This is snippy 4.6.0 [01:21:02] Written by Torsten Seemann [01:21:02] Obtained from https://github.com/tseemann/snippy [01:21:02] Detected operating system: linux [01:21:02] Enabling bundled linux tools. [01:21:02] Found bwa - /usr/local/bin/bwa [01:21:02] Found bcftools - /usr/local/bin/bcftools [01:21:02] Found samtools - /usr/local/bin/samtools [01:21:02] Found java - /usr/local/bin/java [01:21:02] Found snpEff - /usr/local/bin/snpEff [01:21:02] Found samclip - /usr/local/bin/samclip [01:21:02] Found seqtk - /usr/local/bin/seqtk [01:21:02] Found parallel - /usr/local/bin/parallel [01:21:02] Found freebayes - /usr/local/bin/freebayes [01:21:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:21:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:21:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:21:02] Found vcfuniq - /usr/local/bin/vcfuniq [01:21:02] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:21:02] Found gzip - /bin/gzip [01:21:02] Found vt - /usr/local/bin/vt [01:21:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:21:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:21:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:21:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:21:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:21:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:21:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:21:03] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:23:28] This is snippy 4.6.0
Show full stderr[01:23:28] This is snippy 4.6.0 [01:23:28] Written by Torsten Seemann [01:23:28] Obtained from https://github.com/tseemann/snippy [01:23:28] Detected operating system: linux [01:23:28] Enabling bundled linux tools. [01:23:28] Found bwa - /usr/local/bin/bwa [01:23:28] Found bcftools - /usr/local/bin/bcftools [01:23:28] Found samtools - /usr/local/bin/samtools [01:23:28] Found java - /usr/local/bin/java [01:23:28] Found snpEff - /usr/local/bin/snpEff [01:23:28] Found samclip - /usr/local/bin/samclip [01:23:28] Found seqtk - /usr/local/bin/seqtk [01:23:28] Found parallel - /usr/local/bin/parallel [01:23:28] Found freebayes - /usr/local/bin/freebayes [01:23:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:23:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:23:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:23:28] Found vcfuniq - /usr/local/bin/vcfuniq [01:23:28] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:23:28] Found gzip - /bin/gzip [01:23:28] Found vt - /usr/local/bin/vt [01:23:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:23:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:23:29] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:23:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:23:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:23:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:23:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:23:29] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:52:53] This is snippy 4.6.0
Show full stderr[01:52:53] This is snippy 4.6.0 [01:52:53] Written by Torsten Seemann [01:52:53] Obtained from https://github.com/tseemann/snippy [01:52:53] Detected operating system: linux [01:52:53] Enabling bundled linux tools. [01:52:53] Found bwa - /usr/local/bin/bwa [01:52:53] Found bcftools - /usr/local/bin/bcftools [01:52:53] Found samtools - /usr/local/bin/samtools [01:52:53] Found java - /usr/local/bin/java [01:52:53] Found snpEff - /usr/local/bin/snpEff [01:52:53] Found samclip - /usr/local/bin/samclip [01:52:53] Found seqtk - /usr/local/bin/seqtk [01:52:53] Found parallel - /usr/local/bin/parallel [01:52:53] Found freebayes - /usr/local/bin/freebayes [01:52:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:52:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:52:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:52:53] Found vcfuniq - /usr/local/bin/vcfuniq [01:52:53] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:52:53] Found gzip - /bin/gzip [01:52:53] Found vt - /usr/local/bin/vt [01:52:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:52:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:52:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:52:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:52:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:52:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:52:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:52:56] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:23:51] This is snippy 4.6.0
Show full stderr[01:23:51] This is snippy 4.6.0 [01:23:51] Written by Torsten Seemann [01:23:51] Obtained from https://github.com/tseemann/snippy [01:23:51] Detected operating system: linux [01:23:51] Enabling bundled linux tools. [01:23:51] Found bwa - /usr/local/bin/bwa [01:23:51] Found bcftools - /usr/local/bin/bcftools [01:23:51] Found samtools - /usr/local/bin/samtools [01:23:51] Found java - /usr/local/bin/java [01:23:51] Found snpEff - /usr/local/bin/snpEff [01:23:51] Found samclip - /usr/local/bin/samclip [01:23:51] Found seqtk - /usr/local/bin/seqtk [01:23:51] Found parallel - /usr/local/bin/parallel [01:23:51] Found freebayes - /usr/local/bin/freebayes [01:23:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:23:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:23:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:23:51] Found vcfuniq - /usr/local/bin/vcfuniq [01:23:52] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:23:52] Found gzip - /bin/gzip [01:23:52] Found vt - /usr/local/bin/vt [01:23:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:23:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:23:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:23:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:23:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:23:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:23:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:23:52] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:31:09] This is snippy 4.6.0
Show full stderr[00:31:09] This is snippy 4.6.0 [00:31:09] Written by Torsten Seemann [00:31:09] Obtained from https://github.com/tseemann/snippy [00:31:09] Detected operating system: linux [00:31:09] Enabling bundled linux tools. [00:31:09] Found bwa - /usr/local/bin/bwa [00:31:09] Found bcftools - /usr/local/bin/bcftools [00:31:09] Found samtools - /usr/local/bin/samtools [00:31:09] Found java - /usr/local/bin/java [00:31:09] Found snpEff - /usr/local/bin/snpEff [00:31:09] Found samclip - /usr/local/bin/samclip [00:31:09] Found seqtk - /usr/local/bin/seqtk [00:31:09] Found parallel - /usr/local/bin/parallel [00:31:09] Found freebayes - /usr/local/bin/freebayes [00:31:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:31:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:31:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:31:09] Found vcfuniq - /usr/local/bin/vcfuniq [00:31:09] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:31:09] Found gzip - /bin/gzip [00:31:09] Found vt - /usr/local/bin/vt [00:31:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:31:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:31:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:31:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:31:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:31:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:31:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:31:10] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:31:48] This is snippy 4.6.0
Show full stderr[00:31:48] This is snippy 4.6.0 [00:31:48] Written by Torsten Seemann [00:31:48] Obtained from https://github.com/tseemann/snippy [00:31:48] Detected operating system: linux [00:31:48] Enabling bundled linux tools. [00:31:48] Found bwa - /usr/local/bin/bwa [00:31:48] Found bcftools - /usr/local/bin/bcftools [00:31:48] Found samtools - /usr/local/bin/samtools [00:31:48] Found java - /usr/local/bin/java [00:31:48] Found snpEff - /usr/local/bin/snpEff [00:31:48] Found samclip - /usr/local/bin/samclip [00:31:48] Found seqtk - /usr/local/bin/seqtk [00:31:48] Found parallel - /usr/local/bin/parallel [00:31:48] Found freebayes - /usr/local/bin/freebayes [00:31:48] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:31:48] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:31:48] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:31:48] Found vcfuniq - /usr/local/bin/vcfuniq [00:31:48] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:31:48] Found gzip - /bin/gzip [00:31:48] Found vt - /usr/local/bin/vt [00:31:48] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:31:48] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:31:48] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:31:48] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:31:48] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:31:49] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:31:49] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:31:49] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:41:26] This is snippy 4.6.0
Show full stderr[00:41:26] This is snippy 4.6.0 [00:41:26] Written by Torsten Seemann [00:41:26] Obtained from https://github.com/tseemann/snippy [00:41:26] Detected operating system: linux [00:41:26] Enabling bundled linux tools. [00:41:26] Found bwa - /usr/local/bin/bwa [00:41:26] Found bcftools - /usr/local/bin/bcftools [00:41:26] Found samtools - /usr/local/bin/samtools [00:41:26] Found java - /usr/local/bin/java [00:41:26] Found snpEff - /usr/local/bin/snpEff [00:41:26] Found samclip - /usr/local/bin/samclip [00:41:26] Found seqtk - /usr/local/bin/seqtk [00:41:26] Found parallel - /usr/local/bin/parallel [00:41:26] Found freebayes - /usr/local/bin/freebayes [00:41:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:41:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:41:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:41:26] Found vcfuniq - /usr/local/bin/vcfuniq [00:41:26] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:41:26] Found gzip - /bin/gzip [00:41:26] Found vt - /usr/local/bin/vt [00:41:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:41:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:41:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:41:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:41:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:41:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:41:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:41:27] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:31:58] This is snippy 4.6.0
Show full stderr[00:31:58] This is snippy 4.6.0 [00:31:58] Written by Torsten Seemann [00:31:58] Obtained from https://github.com/tseemann/snippy [00:31:58] Detected operating system: linux [00:31:58] Enabling bundled linux tools. [00:31:58] Found bwa - /usr/local/bin/bwa [00:31:58] Found bcftools - /usr/local/bin/bcftools [00:31:58] Found samtools - /usr/local/bin/samtools [00:31:58] Found java - /usr/local/bin/java [00:31:58] Found snpEff - /usr/local/bin/snpEff [00:31:58] Found samclip - /usr/local/bin/samclip [00:31:58] Found seqtk - /usr/local/bin/seqtk [00:31:58] Found parallel - /usr/local/bin/parallel [00:31:58] Found freebayes - /usr/local/bin/freebayes [00:31:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:31:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:31:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:31:58] Found vcfuniq - /usr/local/bin/vcfuniq [00:31:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:31:58] Found gzip - /bin/gzip [00:31:58] Found vt - /usr/local/bin/vt [00:31:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:31:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:31:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:31:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:31:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:31:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:31:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:31:59] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:41:39] This is snippy 4.6.0
Show full stderr[00:41:39] This is snippy 4.6.0 [00:41:39] Written by Torsten Seemann [00:41:39] Obtained from https://github.com/tseemann/snippy [00:41:39] Detected operating system: linux [00:41:39] Enabling bundled linux tools. [00:41:39] Found bwa - /usr/local/bin/bwa [00:41:39] Found bcftools - /usr/local/bin/bcftools [00:41:39] Found samtools - /usr/local/bin/samtools [00:41:39] Found java - /usr/local/bin/java [00:41:39] Found snpEff - /usr/local/bin/snpEff [00:41:39] Found samclip - /usr/local/bin/samclip [00:41:39] Found seqtk - /usr/local/bin/seqtk [00:41:39] Found parallel - /usr/local/bin/parallel [00:41:39] Found freebayes - /usr/local/bin/freebayes [00:41:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:41:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:41:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:41:39] Found vcfuniq - /usr/local/bin/vcfuniq [00:41:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:41:39] Found gzip - /bin/gzip [00:41:39] Found vt - /usr/local/bin/vt [00:41:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:41:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:41:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:41:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:41:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:41:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:41:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:41:40] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:32:01] This is snippy 4.6.0
Show full stderr[00:32:01] This is snippy 4.6.0 [00:32:01] Written by Torsten Seemann [00:32:01] Obtained from https://github.com/tseemann/snippy [00:32:01] Detected operating system: linux [00:32:01] Enabling bundled linux tools. [00:32:01] Found bwa - /usr/local/bin/bwa [00:32:01] Found bcftools - /usr/local/bin/bcftools [00:32:01] Found samtools - /usr/local/bin/samtools [00:32:01] Found java - /usr/local/bin/java [00:32:01] Found snpEff - /usr/local/bin/snpEff [00:32:01] Found samclip - /usr/local/bin/samclip [00:32:01] Found seqtk - /usr/local/bin/seqtk [00:32:01] Found parallel - /usr/local/bin/parallel [00:32:01] Found freebayes - /usr/local/bin/freebayes [00:32:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:32:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:32:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:32:01] Found vcfuniq - /usr/local/bin/vcfuniq [00:32:01] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:32:01] Found gzip - /bin/gzip [00:32:01] Found vt - /usr/local/bin/vt [00:32:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:32:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:32:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:32:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:32:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:32:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:32:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:32:02] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:42:13] This is snippy 4.6.0
Show full stderr[00:42:13] This is snippy 4.6.0 [00:42:13] Written by Torsten Seemann [00:42:13] Obtained from https://github.com/tseemann/snippy [00:42:13] Detected operating system: linux [00:42:13] Enabling bundled linux tools. [00:42:13] Found bwa - /usr/local/bin/bwa [00:42:13] Found bcftools - /usr/local/bin/bcftools [00:42:13] Found samtools - /usr/local/bin/samtools [00:42:13] Found java - /usr/local/bin/java [00:42:13] Found snpEff - /usr/local/bin/snpEff [00:42:13] Found samclip - /usr/local/bin/samclip [00:42:13] Found seqtk - /usr/local/bin/seqtk [00:42:13] Found parallel - /usr/local/bin/parallel [00:42:13] Found freebayes - /usr/local/bin/freebayes [00:42:13] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:42:13] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:42:13] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:42:13] Found vcfuniq - /usr/local/bin/vcfuniq [00:42:13] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:42:13] Found gzip - /bin/gzip [00:42:13] Found vt - /usr/local/bin/vt [00:42:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:42:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:42:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:42:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:42:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:42:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:42:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:42:13] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:32:19] This is snippy 4.6.0
Show full stderr[00:32:19] This is snippy 4.6.0 [00:32:19] Written by Torsten Seemann [00:32:19] Obtained from https://github.com/tseemann/snippy [00:32:19] Detected operating system: linux [00:32:19] Enabling bundled linux tools. [00:32:19] Found bwa - /usr/local/bin/bwa [00:32:19] Found bcftools - /usr/local/bin/bcftools [00:32:19] Found samtools - /usr/local/bin/samtools [00:32:19] Found java - /usr/local/bin/java [00:32:19] Found snpEff - /usr/local/bin/snpEff [00:32:19] Found samclip - /usr/local/bin/samclip [00:32:19] Found seqtk - /usr/local/bin/seqtk [00:32:19] Found parallel - /usr/local/bin/parallel [00:32:19] Found freebayes - /usr/local/bin/freebayes [00:32:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:32:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:32:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:32:19] Found vcfuniq - /usr/local/bin/vcfuniq [00:32:19] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:32:19] Found gzip - /bin/gzip [00:32:19] Found vt - /usr/local/bin/vt [00:32:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:32:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:32:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:32:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:32:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:32:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:32:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:32:20] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:32:34] This is snippy 4.6.0
Show full stderr[00:32:34] This is snippy 4.6.0 [00:32:34] Written by Torsten Seemann [00:32:34] Obtained from https://github.com/tseemann/snippy [00:32:34] Detected operating system: linux [00:32:34] Enabling bundled linux tools. [00:32:34] Found bwa - /usr/local/bin/bwa [00:32:34] Found bcftools - /usr/local/bin/bcftools [00:32:34] Found samtools - /usr/local/bin/samtools [00:32:34] Found java - /usr/local/bin/java [00:32:34] Found snpEff - /usr/local/bin/snpEff [00:32:34] Found samclip - /usr/local/bin/samclip [00:32:34] Found seqtk - /usr/local/bin/seqtk [00:32:34] Found parallel - /usr/local/bin/parallel [00:32:34] Found freebayes - /usr/local/bin/freebayes [00:32:34] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:32:34] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:32:34] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:32:34] Found vcfuniq - /usr/local/bin/vcfuniq [00:32:34] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:32:34] Found gzip - /bin/gzip [00:32:34] Found vt - /usr/local/bin/vt [00:32:34] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:32:34] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:32:34] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:32:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:32:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:32:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:32:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:32:35] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:59:36] This is snippy 4.6.0
Show full stderr[00:59:36] This is snippy 4.6.0 [00:59:36] Written by Torsten Seemann [00:59:36] Obtained from https://github.com/tseemann/snippy [00:59:36] Detected operating system: linux [00:59:36] Enabling bundled linux tools. [00:59:36] Found bwa - /usr/local/bin/bwa [00:59:36] Found bcftools - /usr/local/bin/bcftools [00:59:36] Found samtools - /usr/local/bin/samtools [00:59:36] Found java - /usr/local/bin/java [00:59:36] Found snpEff - /usr/local/bin/snpEff [00:59:36] Found samclip - /usr/local/bin/samclip [00:59:36] Found seqtk - /usr/local/bin/seqtk [00:59:36] Found parallel - /usr/local/bin/parallel [00:59:36] Found freebayes - /usr/local/bin/freebayes [00:59:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:59:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:59:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:59:36] Found vcfuniq - /usr/local/bin/vcfuniq [00:59:36] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:59:36] Found gzip - /bin/gzip [00:59:36] Found vt - /usr/local/bin/vt [00:59:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:59:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:59:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:59:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:59:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:59:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:59:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:59:37] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:00:38] This is snippy 4.6.0
Show full stderr[01:00:38] This is snippy 4.6.0 [01:00:38] Written by Torsten Seemann [01:00:38] Obtained from https://github.com/tseemann/snippy [01:00:38] Detected operating system: linux [01:00:38] Enabling bundled linux tools. [01:00:38] Found bwa - /usr/local/bin/bwa [01:00:38] Found bcftools - /usr/local/bin/bcftools [01:00:38] Found samtools - /usr/local/bin/samtools [01:00:38] Found java - /usr/local/bin/java [01:00:38] Found snpEff - /usr/local/bin/snpEff [01:00:38] Found samclip - /usr/local/bin/samclip [01:00:38] Found seqtk - /usr/local/bin/seqtk [01:00:38] Found parallel - /usr/local/bin/parallel [01:00:38] Found freebayes - /usr/local/bin/freebayes [01:00:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:00:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:00:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:00:38] Found vcfuniq - /usr/local/bin/vcfuniq [01:00:38] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:00:38] Found gzip - /bin/gzip [01:00:38] Found vt - /usr/local/bin/vt [01:00:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:00:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:00:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:00:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:00:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:00:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:00:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:00:39] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:05:35] This is snippy 4.6.0
Show full stderr[01:05:35] This is snippy 4.6.0 [01:05:35] Written by Torsten Seemann [01:05:35] Obtained from https://github.com/tseemann/snippy [01:05:35] Detected operating system: linux [01:05:35] Enabling bundled linux tools. [01:05:35] Found bwa - /usr/local/bin/bwa [01:05:35] Found bcftools - /usr/local/bin/bcftools [01:05:35] Found samtools - /usr/local/bin/samtools [01:05:35] Found java - /usr/local/bin/java [01:05:35] Found snpEff - /usr/local/bin/snpEff [01:05:35] Found samclip - /usr/local/bin/samclip [01:05:35] Found seqtk - /usr/local/bin/seqtk [01:05:35] Found parallel - /usr/local/bin/parallel [01:05:35] Found freebayes - /usr/local/bin/freebayes [01:05:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:05:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:05:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:05:35] Found vcfuniq - /usr/local/bin/vcfuniq [01:05:35] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:05:35] Found gzip - /bin/gzip [01:05:36] Found vt - /usr/local/bin/vt [01:05:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:05:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:05:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:05:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:05:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:05:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:05:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:05:38] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:07:03] This is snippy 4.6.0
Show full stderr[01:07:03] This is snippy 4.6.0 [01:07:03] Written by Torsten Seemann [01:07:03] Obtained from https://github.com/tseemann/snippy [01:07:03] Detected operating system: linux [01:07:03] Enabling bundled linux tools. [01:07:03] Found bwa - /usr/local/bin/bwa [01:07:03] Found bcftools - /usr/local/bin/bcftools [01:07:03] Found samtools - /usr/local/bin/samtools [01:07:03] Found java - /usr/local/bin/java [01:07:03] Found snpEff - /usr/local/bin/snpEff [01:07:03] Found samclip - /usr/local/bin/samclip [01:07:03] Found seqtk - /usr/local/bin/seqtk [01:07:03] Found parallel - /usr/local/bin/parallel [01:07:03] Found freebayes - /usr/local/bin/freebayes [01:07:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:07:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:07:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:07:03] Found vcfuniq - /usr/local/bin/vcfuniq [01:07:03] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:07:03] Found gzip - /bin/gzip [01:07:03] Found vt - /usr/local/bin/vt [01:07:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:07:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:07:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:07:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:07:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:07:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:07:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:07:04] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:12:27] This is snippy 4.6.0
Show full stderr[01:12:27] This is snippy 4.6.0 [01:12:27] Written by Torsten Seemann [01:12:27] Obtained from https://github.com/tseemann/snippy [01:12:27] Detected operating system: linux [01:12:27] Enabling bundled linux tools. [01:12:27] Found bwa - /usr/local/bin/bwa [01:12:27] Found bcftools - /usr/local/bin/bcftools [01:12:27] Found samtools - /usr/local/bin/samtools [01:12:27] Found java - /usr/local/bin/java [01:12:27] Found snpEff - /usr/local/bin/snpEff [01:12:27] Found samclip - /usr/local/bin/samclip [01:12:27] Found seqtk - /usr/local/bin/seqtk [01:12:27] Found parallel - /usr/local/bin/parallel [01:12:27] Found freebayes - /usr/local/bin/freebayes [01:12:27] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:12:27] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:12:27] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:12:27] Found vcfuniq - /usr/local/bin/vcfuniq [01:12:27] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:12:27] Found gzip - /bin/gzip [01:12:27] Found vt - /usr/local/bin/vt [01:12:27] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:12:27] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:12:27] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:12:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:12:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:12:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:12:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:12:27] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:47:57] This is snippy 4.6.0
Show full stderr[01:47:57] This is snippy 4.6.0 [01:47:57] Written by Torsten Seemann [01:47:57] Obtained from https://github.com/tseemann/snippy [01:47:57] Detected operating system: linux [01:47:57] Enabling bundled linux tools. [01:47:57] Found bwa - /usr/local/bin/bwa [01:47:57] Found bcftools - /usr/local/bin/bcftools [01:47:57] Found samtools - /usr/local/bin/samtools [01:47:57] Found java - /usr/local/bin/java [01:47:57] Found snpEff - /usr/local/bin/snpEff [01:47:57] Found samclip - /usr/local/bin/samclip [01:47:57] Found seqtk - /usr/local/bin/seqtk [01:47:57] Found parallel - /usr/local/bin/parallel [01:47:57] Found freebayes - /usr/local/bin/freebayes [01:47:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:47:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:47:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:47:57] Found vcfuniq - /usr/local/bin/vcfuniq [01:47:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:47:57] Found gzip - /bin/gzip [01:47:57] Found vt - /usr/local/bin/vt [01:47:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:47:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:47:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:47:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:47:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:47:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:47:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:47:59] Please supply a reference FASTA/GBK/EMBL file with --reference
1[02:06:28] This is snippy 4.6.0
Show full stderr[02:06:28] This is snippy 4.6.0 [02:06:28] Written by Torsten Seemann [02:06:28] Obtained from https://github.com/tseemann/snippy [02:06:28] Detected operating system: linux [02:06:28] Enabling bundled linux tools. [02:06:28] Found bwa - /usr/local/bin/bwa [02:06:28] Found bcftools - /usr/local/bin/bcftools [02:06:28] Found samtools - /usr/local/bin/samtools [02:06:28] Found java - /usr/local/bin/java [02:06:28] Found snpEff - /usr/local/bin/snpEff [02:06:28] Found samclip - /usr/local/bin/samclip [02:06:28] Found seqtk - /usr/local/bin/seqtk [02:06:28] Found parallel - /usr/local/bin/parallel [02:06:28] Found freebayes - /usr/local/bin/freebayes [02:06:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [02:06:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [02:06:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [02:06:28] Found vcfuniq - /usr/local/bin/vcfuniq [02:06:28] Found vcffirstheader - /usr/local/bin/vcffirstheader [02:06:28] Found gzip - /bin/gzip [02:06:28] Found vt - /usr/local/bin/vt [02:06:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [02:06:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [02:06:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [02:06:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [02:06:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [02:06:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [02:06:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [02:06:29] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:48:12] This is snippy 4.6.0
Show full stderr[01:48:12] This is snippy 4.6.0 [01:48:12] Written by Torsten Seemann [01:48:12] Obtained from https://github.com/tseemann/snippy [01:48:12] Detected operating system: linux [01:48:12] Enabling bundled linux tools. [01:48:12] Found bwa - /usr/local/bin/bwa [01:48:12] Found bcftools - /usr/local/bin/bcftools [01:48:12] Found samtools - /usr/local/bin/samtools [01:48:12] Found java - /usr/local/bin/java [01:48:12] Found snpEff - /usr/local/bin/snpEff [01:48:12] Found samclip - /usr/local/bin/samclip [01:48:12] Found seqtk - /usr/local/bin/seqtk [01:48:12] Found parallel - /usr/local/bin/parallel [01:48:12] Found freebayes - /usr/local/bin/freebayes [01:48:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:48:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:48:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:48:12] Found vcfuniq - /usr/local/bin/vcfuniq [01:48:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:48:12] Found gzip - /bin/gzip [01:48:12] Found vt - /usr/local/bin/vt [01:48:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:48:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:48:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:48:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:48:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:48:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:48:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:48:13] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:48:31] This is snippy 4.6.0
Show full stderr[01:48:31] This is snippy 4.6.0 [01:48:31] Written by Torsten Seemann [01:48:31] Obtained from https://github.com/tseemann/snippy [01:48:31] Detected operating system: linux [01:48:31] Enabling bundled linux tools. [01:48:31] Found bwa - /usr/local/bin/bwa [01:48:31] Found bcftools - /usr/local/bin/bcftools [01:48:31] Found samtools - /usr/local/bin/samtools [01:48:31] Found java - /usr/local/bin/java [01:48:31] Found snpEff - /usr/local/bin/snpEff [01:48:31] Found samclip - /usr/local/bin/samclip [01:48:31] Found seqtk - /usr/local/bin/seqtk [01:48:31] Found parallel - /usr/local/bin/parallel [01:48:31] Found freebayes - /usr/local/bin/freebayes [01:48:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:48:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:48:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:48:31] Found vcfuniq - /usr/local/bin/vcfuniq [01:48:31] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:48:31] Found gzip - /bin/gzip [01:48:31] Found vt - /usr/local/bin/vt [01:48:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:48:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:48:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:48:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:48:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:48:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:48:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:48:32] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:50:49] This is snippy 4.6.0
Show full stderr[01:50:49] This is snippy 4.6.0 [01:50:49] Written by Torsten Seemann [01:50:49] Obtained from https://github.com/tseemann/snippy [01:50:49] Detected operating system: linux [01:50:49] Enabling bundled linux tools. [01:50:49] Found bwa - /usr/local/bin/bwa [01:50:49] Found bcftools - /usr/local/bin/bcftools [01:50:49] Found samtools - /usr/local/bin/samtools [01:50:49] Found java - /usr/local/bin/java [01:50:49] Found snpEff - /usr/local/bin/snpEff [01:50:49] Found samclip - /usr/local/bin/samclip [01:50:49] Found seqtk - /usr/local/bin/seqtk [01:50:49] Found parallel - /usr/local/bin/parallel [01:50:49] Found freebayes - /usr/local/bin/freebayes [01:50:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:50:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:50:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:50:49] Found vcfuniq - /usr/local/bin/vcfuniq [01:50:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:50:49] Found gzip - /bin/gzip [01:50:49] Found vt - /usr/local/bin/vt [01:50:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:50:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:50:50] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:50:50] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:50:50] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:50:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:50:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:50:51] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:56:27] This is snippy 4.6.0
Show full stderr[01:56:27] This is snippy 4.6.0 [01:56:27] Written by Torsten Seemann [01:56:27] Obtained from https://github.com/tseemann/snippy [01:56:27] Detected operating system: linux [01:56:27] Enabling bundled linux tools. [01:56:27] Found bwa - /usr/local/bin/bwa [01:56:27] Found bcftools - /usr/local/bin/bcftools [01:56:27] Found samtools - /usr/local/bin/samtools [01:56:27] Found java - /usr/local/bin/java [01:56:27] Found snpEff - /usr/local/bin/snpEff [01:56:28] Found samclip - /usr/local/bin/samclip [01:56:28] Found seqtk - /usr/local/bin/seqtk [01:56:28] Found parallel - /usr/local/bin/parallel [01:56:28] Found freebayes - /usr/local/bin/freebayes [01:56:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:56:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:56:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:56:28] Found vcfuniq - /usr/local/bin/vcfuniq [01:56:28] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:56:28] Found gzip - /bin/gzip [01:56:28] Found vt - /usr/local/bin/vt [01:56:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:56:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:56:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:56:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:56:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:56:28] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:56:28] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:56:28] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:58:23] This is snippy 4.6.0
Show full stderr[01:58:23] This is snippy 4.6.0 [01:58:23] Written by Torsten Seemann [01:58:23] Obtained from https://github.com/tseemann/snippy [01:58:23] Detected operating system: linux [01:58:23] Enabling bundled linux tools. [01:58:23] Found bwa - /usr/local/bin/bwa [01:58:23] Found bcftools - /usr/local/bin/bcftools [01:58:23] Found samtools - /usr/local/bin/samtools [01:58:23] Found java - /usr/local/bin/java [01:58:23] Found snpEff - /usr/local/bin/snpEff [01:58:23] Found samclip - /usr/local/bin/samclip [01:58:23] Found seqtk - /usr/local/bin/seqtk [01:58:23] Found parallel - /usr/local/bin/parallel [01:58:23] Found freebayes - /usr/local/bin/freebayes [01:58:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:58:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:58:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:58:23] Found vcfuniq - /usr/local/bin/vcfuniq [01:58:23] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:58:23] Found gzip - /bin/gzip [01:58:23] Found vt - /usr/local/bin/vt [01:58:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:58:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:58:23] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:58:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:58:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:58:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:58:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:58:24] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:58:52] This is snippy 4.6.0
Show full stderr[01:58:52] This is snippy 4.6.0 [01:58:52] Written by Torsten Seemann [01:58:52] Obtained from https://github.com/tseemann/snippy [01:58:52] Detected operating system: linux [01:58:52] Enabling bundled linux tools. [01:58:52] Found bwa - /usr/local/bin/bwa [01:58:52] Found bcftools - /usr/local/bin/bcftools [01:58:52] Found samtools - /usr/local/bin/samtools [01:58:52] Found java - /usr/local/bin/java [01:58:52] Found snpEff - /usr/local/bin/snpEff [01:58:52] Found samclip - /usr/local/bin/samclip [01:58:52] Found seqtk - /usr/local/bin/seqtk [01:58:52] Found parallel - /usr/local/bin/parallel [01:58:52] Found freebayes - /usr/local/bin/freebayes [01:58:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:58:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:58:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:58:52] Found vcfuniq - /usr/local/bin/vcfuniq [01:58:52] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:58:52] Found gzip - /bin/gzip [01:58:52] Found vt - /usr/local/bin/vt [01:58:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:58:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:58:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:58:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:58:52] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:58:53] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:58:53] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:58:53] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:59:00] This is snippy 4.6.0
Show full stderr[01:59:00] This is snippy 4.6.0 [01:59:00] Written by Torsten Seemann [01:59:00] Obtained from https://github.com/tseemann/snippy [01:59:00] Detected operating system: linux [01:59:00] Enabling bundled linux tools. [01:59:00] Found bwa - /usr/local/bin/bwa [01:59:00] Found bcftools - /usr/local/bin/bcftools [01:59:00] Found samtools - /usr/local/bin/samtools [01:59:00] Found java - /usr/local/bin/java [01:59:00] Found snpEff - /usr/local/bin/snpEff [01:59:00] Found samclip - /usr/local/bin/samclip [01:59:00] Found seqtk - /usr/local/bin/seqtk [01:59:00] Found parallel - /usr/local/bin/parallel [01:59:00] Found freebayes - /usr/local/bin/freebayes [01:59:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:59:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:59:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:59:00] Found vcfuniq - /usr/local/bin/vcfuniq [01:59:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:59:00] Found gzip - /bin/gzip [01:59:00] Found vt - /usr/local/bin/vt [01:59:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:59:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:59:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:59:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:59:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:59:01] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:59:01] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:59:01] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:59:09] This is snippy 4.6.0
Show full stderr[01:59:09] This is snippy 4.6.0 [01:59:09] Written by Torsten Seemann [01:59:09] Obtained from https://github.com/tseemann/snippy [01:59:09] Detected operating system: linux [01:59:09] Enabling bundled linux tools. [01:59:09] Found bwa - /usr/local/bin/bwa [01:59:09] Found bcftools - /usr/local/bin/bcftools [01:59:09] Found samtools - /usr/local/bin/samtools [01:59:09] Found java - /usr/local/bin/java [01:59:09] Found snpEff - /usr/local/bin/snpEff [01:59:09] Found samclip - /usr/local/bin/samclip [01:59:09] Found seqtk - /usr/local/bin/seqtk [01:59:09] Found parallel - /usr/local/bin/parallel [01:59:09] Found freebayes - /usr/local/bin/freebayes [01:59:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:59:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:59:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:59:09] Found vcfuniq - /usr/local/bin/vcfuniq [01:59:09] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:59:09] Found gzip - /bin/gzip [01:59:09] Found vt - /usr/local/bin/vt [01:59:09] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:59:09] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:59:09] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:59:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:59:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:59:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:59:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:59:10] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:59:16] This is snippy 4.6.0
Show full stderr[01:59:16] This is snippy 4.6.0 [01:59:16] Written by Torsten Seemann [01:59:16] Obtained from https://github.com/tseemann/snippy [01:59:16] Detected operating system: linux [01:59:16] Enabling bundled linux tools. [01:59:16] Found bwa - /usr/local/bin/bwa [01:59:16] Found bcftools - /usr/local/bin/bcftools [01:59:16] Found samtools - /usr/local/bin/samtools [01:59:16] Found java - /usr/local/bin/java [01:59:16] Found snpEff - /usr/local/bin/snpEff [01:59:16] Found samclip - /usr/local/bin/samclip [01:59:16] Found seqtk - /usr/local/bin/seqtk [01:59:16] Found parallel - /usr/local/bin/parallel [01:59:16] Found freebayes - /usr/local/bin/freebayes [01:59:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:59:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:59:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:59:16] Found vcfuniq - /usr/local/bin/vcfuniq [01:59:16] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:59:16] Found gzip - /bin/gzip [01:59:16] Found vt - /usr/local/bin/vt [01:59:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:59:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:59:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:59:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:59:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:59:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:59:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:59:17] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:59:31] This is snippy 4.6.0
Show full stderr[01:59:31] This is snippy 4.6.0 [01:59:31] Written by Torsten Seemann [01:59:31] Obtained from https://github.com/tseemann/snippy [01:59:31] Detected operating system: linux [01:59:31] Enabling bundled linux tools. [01:59:31] Found bwa - /usr/local/bin/bwa [01:59:31] Found bcftools - /usr/local/bin/bcftools [01:59:31] Found samtools - /usr/local/bin/samtools [01:59:31] Found java - /usr/local/bin/java [01:59:31] Found snpEff - /usr/local/bin/snpEff [01:59:31] Found samclip - /usr/local/bin/samclip [01:59:31] Found seqtk - /usr/local/bin/seqtk [01:59:31] Found parallel - /usr/local/bin/parallel [01:59:31] Found freebayes - /usr/local/bin/freebayes [01:59:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:59:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:59:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:59:31] Found vcfuniq - /usr/local/bin/vcfuniq [01:59:31] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:59:31] Found gzip - /bin/gzip [01:59:31] Found vt - /usr/local/bin/vt [01:59:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:59:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:59:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:59:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:59:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:59:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:59:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:59:32] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:59:54] This is snippy 4.6.0
Show full stderr[01:59:54] This is snippy 4.6.0 [01:59:54] Written by Torsten Seemann [01:59:54] Obtained from https://github.com/tseemann/snippy [01:59:54] Detected operating system: linux [01:59:54] Enabling bundled linux tools. [01:59:54] Found bwa - /usr/local/bin/bwa [01:59:54] Found bcftools - /usr/local/bin/bcftools [01:59:54] Found samtools - /usr/local/bin/samtools [01:59:54] Found java - /usr/local/bin/java [01:59:54] Found snpEff - /usr/local/bin/snpEff [01:59:54] Found samclip - /usr/local/bin/samclip [01:59:54] Found seqtk - /usr/local/bin/seqtk [01:59:54] Found parallel - /usr/local/bin/parallel [01:59:54] Found freebayes - /usr/local/bin/freebayes [01:59:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:59:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:59:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:59:54] Found vcfuniq - /usr/local/bin/vcfuniq [01:59:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:59:54] Found gzip - /bin/gzip [01:59:54] Found vt - /usr/local/bin/vt [01:59:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:59:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:59:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:59:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:59:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:59:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:59:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:59:55] Please supply a reference FASTA/GBK/EMBL file with --reference
1[02:00:42] This is snippy 4.6.0
Show full stderr[02:00:42] This is snippy 4.6.0 [02:00:42] Written by Torsten Seemann [02:00:42] Obtained from https://github.com/tseemann/snippy [02:00:42] Detected operating system: linux [02:00:42] Enabling bundled linux tools. [02:00:42] Found bwa - /usr/local/bin/bwa [02:00:42] Found bcftools - /usr/local/bin/bcftools [02:00:42] Found samtools - /usr/local/bin/samtools [02:00:42] Found java - /usr/local/bin/java [02:00:42] Found snpEff - /usr/local/bin/snpEff [02:00:42] Found samclip - /usr/local/bin/samclip [02:00:42] Found seqtk - /usr/local/bin/seqtk [02:00:42] Found parallel - /usr/local/bin/parallel [02:00:42] Found freebayes - /usr/local/bin/freebayes [02:00:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [02:00:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [02:00:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [02:00:42] Found vcfuniq - /usr/local/bin/vcfuniq [02:00:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [02:00:42] Found gzip - /bin/gzip [02:00:42] Found vt - /usr/local/bin/vt [02:00:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [02:00:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [02:00:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [02:00:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [02:00:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [02:00:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [02:00:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [02:00:43] Please supply a reference FASTA/GBK/EMBL file with --reference
1[02:02:42] This is snippy 4.6.0
Show full stderr[02:02:42] This is snippy 4.6.0 [02:02:42] Written by Torsten Seemann [02:02:42] Obtained from https://github.com/tseemann/snippy [02:02:42] Detected operating system: linux [02:02:42] Enabling bundled linux tools. [02:02:42] Found bwa - /usr/local/bin/bwa [02:02:42] Found bcftools - /usr/local/bin/bcftools [02:02:42] Found samtools - /usr/local/bin/samtools [02:02:42] Found java - /usr/local/bin/java [02:02:42] Found snpEff - /usr/local/bin/snpEff [02:02:42] Found samclip - /usr/local/bin/samclip [02:02:42] Found seqtk - /usr/local/bin/seqtk [02:02:42] Found parallel - /usr/local/bin/parallel [02:02:42] Found freebayes - /usr/local/bin/freebayes [02:02:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [02:02:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [02:02:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [02:02:42] Found vcfuniq - /usr/local/bin/vcfuniq [02:02:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [02:02:42] Found gzip - /bin/gzip [02:02:42] Found vt - /usr/local/bin/vt [02:02:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [02:02:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [02:02:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [02:02:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [02:02:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [02:02:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [02:02:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [02:02:43] Please supply a reference FASTA/GBK/EMBL file with --reference
1[02:03:57] This is snippy 4.6.0
Show full stderr[02:03:57] This is snippy 4.6.0 [02:03:57] Written by Torsten Seemann [02:03:57] Obtained from https://github.com/tseemann/snippy [02:03:57] Detected operating system: linux [02:03:57] Enabling bundled linux tools. [02:03:58] Found bwa - /usr/local/bin/bwa [02:03:58] Found bcftools - /usr/local/bin/bcftools [02:03:58] Found samtools - /usr/local/bin/samtools [02:03:58] Found java - /usr/local/bin/java [02:03:58] Found snpEff - /usr/local/bin/snpEff [02:03:58] Found samclip - /usr/local/bin/samclip [02:03:58] Found seqtk - /usr/local/bin/seqtk [02:03:58] Found parallel - /usr/local/bin/parallel [02:03:58] Found freebayes - /usr/local/bin/freebayes [02:03:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [02:03:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [02:03:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [02:03:58] Found vcfuniq - /usr/local/bin/vcfuniq [02:03:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [02:03:58] Found gzip - /bin/gzip [02:03:58] Found vt - /usr/local/bin/vt [02:03:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [02:03:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [02:03:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [02:03:59] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [02:03:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [02:04:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [02:04:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [02:04:00] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:49:02] This is snippy 4.6.0
Show full stderr[00:49:02] This is snippy 4.6.0 [00:49:02] Written by Torsten Seemann [00:49:02] Obtained from https://github.com/tseemann/snippy [00:49:02] Detected operating system: linux [00:49:02] Enabling bundled linux tools. [00:49:02] Found bwa - /usr/local/bin/bwa [00:49:02] Found bcftools - /usr/local/bin/bcftools [00:49:02] Found samtools - /usr/local/bin/samtools [00:49:02] Found java - /usr/local/bin/java [00:49:02] Found snpEff - /usr/local/bin/snpEff [00:49:02] Found samclip - /usr/local/bin/samclip [00:49:02] Found seqtk - /usr/local/bin/seqtk [00:49:02] Found parallel - /usr/local/bin/parallel [00:49:02] Found freebayes - /usr/local/bin/freebayes [00:49:02] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:49:02] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:49:02] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:49:02] Found vcfuniq - /usr/local/bin/vcfuniq [00:49:02] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:49:02] Found gzip - /bin/gzip [00:49:02] Found vt - /usr/local/bin/vt [00:49:02] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:49:02] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:49:02] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:49:02] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:49:02] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:49:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:49:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:49:03] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:53:22] This is snippy 4.6.0
Show full stderr[00:53:22] This is snippy 4.6.0 [00:53:22] Written by Torsten Seemann [00:53:22] Obtained from https://github.com/tseemann/snippy [00:53:22] Detected operating system: linux [00:53:22] Enabling bundled linux tools. [00:53:22] Found bwa - /usr/local/bin/bwa [00:53:22] Found bcftools - /usr/local/bin/bcftools [00:53:22] Found samtools - /usr/local/bin/samtools [00:53:22] Found java - /usr/local/bin/java [00:53:22] Found snpEff - /usr/local/bin/snpEff [00:53:22] Found samclip - /usr/local/bin/samclip [00:53:22] Found seqtk - /usr/local/bin/seqtk [00:53:22] Found parallel - /usr/local/bin/parallel [00:53:22] Found freebayes - /usr/local/bin/freebayes [00:53:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:53:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:53:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:53:22] Found vcfuniq - /usr/local/bin/vcfuniq [00:53:22] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:53:22] Found gzip - /bin/gzip [00:53:22] Found vt - /usr/local/bin/vt [00:53:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:53:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:53:23] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:53:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:53:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:53:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:53:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:53:23] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:07:35] This is snippy 4.6.0
Show full stderr[01:07:35] This is snippy 4.6.0 [01:07:35] Written by Torsten Seemann [01:07:35] Obtained from https://github.com/tseemann/snippy [01:07:35] Detected operating system: linux [01:07:35] Enabling bundled linux tools. [01:07:36] Found bwa - /usr/local/bin/bwa [01:07:36] Found bcftools - /usr/local/bin/bcftools [01:07:36] Found samtools - /usr/local/bin/samtools [01:07:36] Found java - /usr/local/bin/java [01:07:36] Found snpEff - /usr/local/bin/snpEff [01:07:36] Found samclip - /usr/local/bin/samclip [01:07:36] Found seqtk - /usr/local/bin/seqtk [01:07:36] Found parallel - /usr/local/bin/parallel [01:07:36] Found freebayes - /usr/local/bin/freebayes [01:07:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:07:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:07:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:07:36] Found vcfuniq - /usr/local/bin/vcfuniq [01:07:36] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:07:36] Found gzip - /bin/gzip [01:07:36] Found vt - /usr/local/bin/vt [01:07:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:07:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:07:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:07:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:07:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:07:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:07:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:07:37] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:56:40] This is snippy 4.6.0
Show full stderr[00:56:40] This is snippy 4.6.0 [00:56:40] Written by Torsten Seemann [00:56:40] Obtained from https://github.com/tseemann/snippy [00:56:40] Detected operating system: linux [00:56:40] Enabling bundled linux tools. [00:56:40] Found bwa - /usr/local/bin/bwa [00:56:40] Found bcftools - /usr/local/bin/bcftools [00:56:40] Found samtools - /usr/local/bin/samtools [00:56:40] Found java - /usr/local/bin/java [00:56:40] Found snpEff - /usr/local/bin/snpEff [00:56:40] Found samclip - /usr/local/bin/samclip [00:56:40] Found seqtk - /usr/local/bin/seqtk [00:56:40] Found parallel - /usr/local/bin/parallel [00:56:40] Found freebayes - /usr/local/bin/freebayes [00:56:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:56:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:56:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:56:40] Found vcfuniq - /usr/local/bin/vcfuniq [00:56:40] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:56:41] Found gzip - /bin/gzip [00:56:41] Found vt - /usr/local/bin/vt [00:56:41] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:56:41] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:56:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:56:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:56:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:56:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:56:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:56:42] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:34:42] This is snippy 4.6.0
Show full stderr[00:34:42] This is snippy 4.6.0 [00:34:42] Written by Torsten Seemann [00:34:42] Obtained from https://github.com/tseemann/snippy [00:34:42] Detected operating system: linux [00:34:42] Enabling bundled linux tools. [00:34:42] Found bwa - /usr/local/bin/bwa [00:34:42] Found bcftools - /usr/local/bin/bcftools [00:34:42] Found samtools - /usr/local/bin/samtools [00:34:42] Found java - /usr/local/bin/java [00:34:42] Found snpEff - /usr/local/bin/snpEff [00:34:42] Found samclip - /usr/local/bin/samclip [00:34:42] Found seqtk - /usr/local/bin/seqtk [00:34:42] Found parallel - /usr/local/bin/parallel [00:34:42] Found freebayes - /usr/local/bin/freebayes [00:34:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:34:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:34:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:34:42] Found vcfuniq - /usr/local/bin/vcfuniq [00:34:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:34:42] Found gzip - /bin/gzip [00:34:42] Found vt - /usr/local/bin/vt [00:34:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:34:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:34:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:34:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:34:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:34:43] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:34:43] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:34:43] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:34:54] This is snippy 4.6.0
Show full stderr[00:34:54] This is snippy 4.6.0 [00:34:54] Written by Torsten Seemann [00:34:54] Obtained from https://github.com/tseemann/snippy [00:34:54] Detected operating system: linux [00:34:54] Enabling bundled linux tools. [00:34:54] Found bwa - /usr/local/bin/bwa [00:34:54] Found bcftools - /usr/local/bin/bcftools [00:34:54] Found samtools - /usr/local/bin/samtools [00:34:54] Found java - /usr/local/bin/java [00:34:54] Found snpEff - /usr/local/bin/snpEff [00:34:54] Found samclip - /usr/local/bin/samclip [00:34:54] Found seqtk - /usr/local/bin/seqtk [00:34:54] Found parallel - /usr/local/bin/parallel [00:34:54] Found freebayes - /usr/local/bin/freebayes [00:34:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:34:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:34:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:34:54] Found vcfuniq - /usr/local/bin/vcfuniq [00:34:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:34:54] Found gzip - /bin/gzip [00:34:54] Found vt - /usr/local/bin/vt [00:34:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:34:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:34:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:34:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:34:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:34:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:34:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:34:55] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:38:35] This is snippy 4.6.0
Show full stderr[00:38:35] This is snippy 4.6.0 [00:38:35] Written by Torsten Seemann [00:38:35] Obtained from https://github.com/tseemann/snippy [00:38:35] Detected operating system: linux [00:38:35] Enabling bundled linux tools. [00:38:35] Found bwa - /usr/local/bin/bwa [00:38:35] Found bcftools - /usr/local/bin/bcftools [00:38:35] Found samtools - /usr/local/bin/samtools [00:38:35] Found java - /usr/local/bin/java [00:38:35] Found snpEff - /usr/local/bin/snpEff [00:38:35] Found samclip - /usr/local/bin/samclip [00:38:35] Found seqtk - /usr/local/bin/seqtk [00:38:35] Found parallel - /usr/local/bin/parallel [00:38:35] Found freebayes - /usr/local/bin/freebayes [00:38:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:38:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:38:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:38:35] Found vcfuniq - /usr/local/bin/vcfuniq [00:38:35] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:38:35] Found gzip - /bin/gzip [00:38:35] Found vt - /usr/local/bin/vt [00:38:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:38:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:38:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:38:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:38:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:38:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:38:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:38:36] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:43:20] This is snippy 4.6.0
Show full stderr[00:43:20] This is snippy 4.6.0 [00:43:20] Written by Torsten Seemann [00:43:20] Obtained from https://github.com/tseemann/snippy [00:43:20] Detected operating system: linux [00:43:20] Enabling bundled linux tools. [00:43:20] Found bwa - /usr/local/bin/bwa [00:43:20] Found bcftools - /usr/local/bin/bcftools [00:43:20] Found samtools - /usr/local/bin/samtools [00:43:20] Found java - /usr/local/bin/java [00:43:20] Found snpEff - /usr/local/bin/snpEff [00:43:20] Found samclip - /usr/local/bin/samclip [00:43:20] Found seqtk - /usr/local/bin/seqtk [00:43:20] Found parallel - /usr/local/bin/parallel [00:43:20] Found freebayes - /usr/local/bin/freebayes [00:43:20] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:43:20] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:43:20] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:43:20] Found vcfuniq - /usr/local/bin/vcfuniq [00:43:20] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:43:20] Found gzip - /bin/gzip [00:43:20] Found vt - /usr/local/bin/vt [00:43:20] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:43:20] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:43:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:43:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:43:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:43:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:43:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:43:21] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:43:17] This is snippy 4.6.0
Show full stderr[00:43:17] This is snippy 4.6.0 [00:43:17] Written by Torsten Seemann [00:43:17] Obtained from https://github.com/tseemann/snippy [00:43:17] Detected operating system: linux [00:43:17] Enabling bundled linux tools. [00:43:17] Found bwa - /usr/local/bin/bwa [00:43:17] Found bcftools - /usr/local/bin/bcftools [00:43:17] Found samtools - /usr/local/bin/samtools [00:43:17] Found java - /usr/local/bin/java [00:43:18] Found snpEff - /usr/local/bin/snpEff [00:43:18] Found samclip - /usr/local/bin/samclip [00:43:18] Found seqtk - /usr/local/bin/seqtk [00:43:18] Found parallel - /usr/local/bin/parallel [00:43:18] Found freebayes - /usr/local/bin/freebayes [00:43:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:43:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:43:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:43:18] Found vcfuniq - /usr/local/bin/vcfuniq [00:43:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:43:18] Found gzip - /bin/gzip [00:43:18] Found vt - /usr/local/bin/vt [00:43:18] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:43:18] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:43:18] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:43:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:43:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:43:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:43:19] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:43:19] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:06:40] This is snippy 4.6.0
Show full stderr[01:06:40] This is snippy 4.6.0 [01:06:40] Written by Torsten Seemann [01:06:40] Obtained from https://github.com/tseemann/snippy [01:06:40] Detected operating system: linux [01:06:40] Enabling bundled linux tools. [01:06:40] Found bwa - /usr/local/bin/bwa [01:06:40] Found bcftools - /usr/local/bin/bcftools [01:06:40] Found samtools - /usr/local/bin/samtools [01:06:40] Found java - /usr/local/bin/java [01:06:40] Found snpEff - /usr/local/bin/snpEff [01:06:40] Found samclip - /usr/local/bin/samclip [01:06:40] Found seqtk - /usr/local/bin/seqtk [01:06:40] Found parallel - /usr/local/bin/parallel [01:06:40] Found freebayes - /usr/local/bin/freebayes [01:06:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:06:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:06:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:06:40] Found vcfuniq - /usr/local/bin/vcfuniq [01:06:40] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:06:40] Found gzip - /bin/gzip [01:06:40] Found vt - /usr/local/bin/vt [01:06:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:06:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:06:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:06:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:06:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:06:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:06:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:06:41] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:11:56] This is snippy 4.6.0
Show full stderr[01:11:56] This is snippy 4.6.0 [01:11:56] Written by Torsten Seemann [01:11:56] Obtained from https://github.com/tseemann/snippy [01:11:56] Detected operating system: linux [01:11:56] Enabling bundled linux tools. [01:11:56] Found bwa - /usr/local/bin/bwa [01:11:56] Found bcftools - /usr/local/bin/bcftools [01:11:56] Found samtools - /usr/local/bin/samtools [01:11:56] Found java - /usr/local/bin/java [01:11:56] Found snpEff - /usr/local/bin/snpEff [01:11:56] Found samclip - /usr/local/bin/samclip [01:11:56] Found seqtk - /usr/local/bin/seqtk [01:11:56] Found parallel - /usr/local/bin/parallel [01:11:56] Found freebayes - /usr/local/bin/freebayes [01:11:56] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:11:56] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:11:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:11:56] Found vcfuniq - /usr/local/bin/vcfuniq [01:11:56] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:11:56] Found gzip - /bin/gzip [01:11:56] Found vt - /usr/local/bin/vt [01:11:56] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:11:56] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:11:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:11:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:11:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:11:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:11:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:11:57] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:53:38] This is snippy 4.6.0
Show full stderr[01:53:38] This is snippy 4.6.0 [01:53:38] Written by Torsten Seemann [01:53:38] Obtained from https://github.com/tseemann/snippy [01:53:38] Detected operating system: linux [01:53:38] Enabling bundled linux tools. [01:53:38] Found bwa - /usr/local/bin/bwa [01:53:38] Found bcftools - /usr/local/bin/bcftools [01:53:38] Found samtools - /usr/local/bin/samtools [01:53:38] Found java - /usr/local/bin/java [01:53:38] Found snpEff - /usr/local/bin/snpEff [01:53:38] Found samclip - /usr/local/bin/samclip [01:53:38] Found seqtk - /usr/local/bin/seqtk [01:53:38] Found parallel - /usr/local/bin/parallel [01:53:38] Found freebayes - /usr/local/bin/freebayes [01:53:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:53:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:53:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:53:38] Found vcfuniq - /usr/local/bin/vcfuniq [01:53:38] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:53:38] Found gzip - /bin/gzip [01:53:38] Found vt - /usr/local/bin/vt [01:53:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:53:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:53:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:53:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:53:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:53:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:53:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:53:38] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:23:57] This is snippy 4.6.0
Show full stderr[01:23:57] This is snippy 4.6.0 [01:23:57] Written by Torsten Seemann [01:23:57] Obtained from https://github.com/tseemann/snippy [01:23:57] Detected operating system: linux [01:23:57] Enabling bundled linux tools. [01:23:57] Found bwa - /usr/local/bin/bwa [01:23:57] Found bcftools - /usr/local/bin/bcftools [01:23:57] Found samtools - /usr/local/bin/samtools [01:23:57] Found java - /usr/local/bin/java [01:23:57] Found snpEff - /usr/local/bin/snpEff [01:23:57] Found samclip - /usr/local/bin/samclip [01:23:57] Found seqtk - /usr/local/bin/seqtk [01:23:57] Found parallel - /usr/local/bin/parallel [01:23:57] Found freebayes - /usr/local/bin/freebayes [01:23:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:23:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:23:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:23:57] Found vcfuniq - /usr/local/bin/vcfuniq [01:23:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:23:57] Found gzip - /bin/gzip [01:23:57] Found vt - /usr/local/bin/vt [01:23:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:23:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:23:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:23:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:23:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:23:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:23:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:23:58] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:24:01] This is snippy 4.6.0
Show full stderr[01:24:01] This is snippy 4.6.0 [01:24:01] Written by Torsten Seemann [01:24:01] Obtained from https://github.com/tseemann/snippy [01:24:01] Detected operating system: linux [01:24:01] Enabling bundled linux tools. [01:24:01] Found bwa - /usr/local/bin/bwa [01:24:01] Found bcftools - /usr/local/bin/bcftools [01:24:01] Found samtools - /usr/local/bin/samtools [01:24:01] Found java - /usr/local/bin/java [01:24:01] Found snpEff - /usr/local/bin/snpEff [01:24:01] Found samclip - /usr/local/bin/samclip [01:24:01] Found seqtk - /usr/local/bin/seqtk [01:24:01] Found parallel - /usr/local/bin/parallel [01:24:01] Found freebayes - /usr/local/bin/freebayes [01:24:01] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:24:01] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:24:01] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:24:01] Found vcfuniq - /usr/local/bin/vcfuniq [01:24:01] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:24:01] Found gzip - /bin/gzip [01:24:01] Found vt - /usr/local/bin/vt [01:24:01] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:24:01] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:24:01] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:24:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:24:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:24:02] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:24:02] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:24:02] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:24:12] This is snippy 4.6.0
Show full stderr[01:24:12] This is snippy 4.6.0 [01:24:12] Written by Torsten Seemann [01:24:12] Obtained from https://github.com/tseemann/snippy [01:24:12] Detected operating system: linux [01:24:12] Enabling bundled linux tools. [01:24:12] Found bwa - /usr/local/bin/bwa [01:24:12] Found bcftools - /usr/local/bin/bcftools [01:24:12] Found samtools - /usr/local/bin/samtools [01:24:12] Found java - /usr/local/bin/java [01:24:12] Found snpEff - /usr/local/bin/snpEff [01:24:12] Found samclip - /usr/local/bin/samclip [01:24:12] Found seqtk - /usr/local/bin/seqtk [01:24:12] Found parallel - /usr/local/bin/parallel [01:24:12] Found freebayes - /usr/local/bin/freebayes [01:24:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:24:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:24:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:24:12] Found vcfuniq - /usr/local/bin/vcfuniq [01:24:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:24:12] Found gzip - /bin/gzip [01:24:12] Found vt - /usr/local/bin/vt [01:24:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:24:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:24:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:24:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:24:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:24:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:24:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:24:13] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:25:18] This is snippy 4.6.0
Show full stderr[01:25:18] This is snippy 4.6.0 [01:25:18] Written by Torsten Seemann [01:25:18] Obtained from https://github.com/tseemann/snippy [01:25:18] Detected operating system: linux [01:25:18] Enabling bundled linux tools. [01:25:18] Found bwa - /usr/local/bin/bwa [01:25:18] Found bcftools - /usr/local/bin/bcftools [01:25:18] Found samtools - /usr/local/bin/samtools [01:25:18] Found java - /usr/local/bin/java [01:25:18] Found snpEff - /usr/local/bin/snpEff [01:25:18] Found samclip - /usr/local/bin/samclip [01:25:18] Found seqtk - /usr/local/bin/seqtk [01:25:18] Found parallel - /usr/local/bin/parallel [01:25:18] Found freebayes - /usr/local/bin/freebayes [01:25:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:25:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:25:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:25:18] Found vcfuniq - /usr/local/bin/vcfuniq [01:25:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:25:18] Found gzip - /bin/gzip [01:25:19] Found vt - /usr/local/bin/vt [01:25:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:25:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:25:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:25:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:25:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:25:19] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:25:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:25:20] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:57:38] This is snippy 4.6.0
Show full stderr[01:57:38] This is snippy 4.6.0 [01:57:38] Written by Torsten Seemann [01:57:38] Obtained from https://github.com/tseemann/snippy [01:57:38] Detected operating system: linux [01:57:38] Enabling bundled linux tools. [01:57:38] Found bwa - /usr/local/bin/bwa [01:57:38] Found bcftools - /usr/local/bin/bcftools [01:57:38] Found samtools - /usr/local/bin/samtools [01:57:38] Found java - /usr/local/bin/java [01:57:38] Found snpEff - /usr/local/bin/snpEff [01:57:38] Found samclip - /usr/local/bin/samclip [01:57:38] Found seqtk - /usr/local/bin/seqtk [01:57:38] Found parallel - /usr/local/bin/parallel [01:57:38] Found freebayes - /usr/local/bin/freebayes [01:57:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:57:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:57:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:57:38] Found vcfuniq - /usr/local/bin/vcfuniq [01:57:38] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:57:38] Found gzip - /bin/gzip [01:57:38] Found vt - /usr/local/bin/vt [01:57:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:57:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:57:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:57:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:57:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:57:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:57:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:57:39] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:25:55] This is snippy 4.6.0
Show full stderr[01:25:55] This is snippy 4.6.0 [01:25:55] Written by Torsten Seemann [01:25:55] Obtained from https://github.com/tseemann/snippy [01:25:55] Detected operating system: linux [01:25:55] Enabling bundled linux tools. [01:25:55] Found bwa - /usr/local/bin/bwa [01:25:55] Found bcftools - /usr/local/bin/bcftools [01:25:55] Found samtools - /usr/local/bin/samtools [01:25:55] Found java - /usr/local/bin/java [01:25:55] Found snpEff - /usr/local/bin/snpEff [01:25:55] Found samclip - /usr/local/bin/samclip [01:25:55] Found seqtk - /usr/local/bin/seqtk [01:25:55] Found parallel - /usr/local/bin/parallel [01:25:55] Found freebayes - /usr/local/bin/freebayes [01:25:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:25:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:25:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:25:55] Found vcfuniq - /usr/local/bin/vcfuniq [01:25:55] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:25:55] Found gzip - /bin/gzip [01:25:55] Found vt - /usr/local/bin/vt [01:25:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:25:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:25:56] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:25:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:25:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:25:57] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:25:57] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:25:57] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:25:51] This is snippy 4.6.0
Show full stderr[01:25:51] This is snippy 4.6.0 [01:25:51] Written by Torsten Seemann [01:25:51] Obtained from https://github.com/tseemann/snippy [01:25:51] Detected operating system: linux [01:25:51] Enabling bundled linux tools. [01:25:51] Found bwa - /usr/local/bin/bwa [01:25:51] Found bcftools - /usr/local/bin/bcftools [01:25:51] Found samtools - /usr/local/bin/samtools [01:25:51] Found java - /usr/local/bin/java [01:25:51] Found snpEff - /usr/local/bin/snpEff [01:25:51] Found samclip - /usr/local/bin/samclip [01:25:51] Found seqtk - /usr/local/bin/seqtk [01:25:51] Found parallel - /usr/local/bin/parallel [01:25:51] Found freebayes - /usr/local/bin/freebayes [01:25:51] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:25:51] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:25:51] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:25:51] Found vcfuniq - /usr/local/bin/vcfuniq [01:25:51] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:25:51] Found gzip - /bin/gzip [01:25:51] Found vt - /usr/local/bin/vt [01:25:51] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:25:51] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:25:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:25:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:25:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:25:52] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:25:52] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:25:52] Please supply a reference FASTA/GBK/EMBL file with --reference
1[10:15:43] This is snippy 4.6.0
Show full stderr[10:15:43] This is snippy 4.6.0 [10:15:43] Written by Torsten Seemann [10:15:43] Obtained from https://github.com/tseemann/snippy [10:15:43] Detected operating system: linux [10:15:43] Enabling bundled linux tools. [10:15:43] Found bwa - /usr/local/bin/bwa [10:15:43] Found bcftools - /usr/local/bin/bcftools [10:15:43] Found samtools - /usr/local/bin/samtools [10:15:43] Found java - /usr/local/bin/java [10:15:43] Found snpEff - /usr/local/bin/snpEff [10:15:43] Found samclip - /usr/local/bin/samclip [10:15:43] Found seqtk - /usr/local/bin/seqtk [10:15:43] Found parallel - /usr/local/bin/parallel [10:15:43] Found freebayes - /usr/local/bin/freebayes [10:15:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [10:15:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [10:15:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [10:15:43] Found vcfuniq - /usr/local/bin/vcfuniq [10:15:43] Found vcffirstheader - /usr/local/bin/vcffirstheader [10:15:43] Found gzip - /bin/gzip [10:15:43] Found vt - /usr/local/bin/vt [10:15:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [10:15:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [10:15:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [10:16:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [10:16:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [10:16:05] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [10:16:05] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [10:16:05] Using reference: /corral4/main/objects/d/7/6/dataset_d764c547-d517-4ce6-9e7c-25fb605e00f7.dat [10:16:05] Treating reference as 'genbank' format. [10:16:05] Will use 1 CPU cores. [10:16:06] Using read file: /corral4/main/objects/c/7/1/dataset_c711a7bd-3ee2-4f67-a5fb-3c76fa60a96f.dat [10:16:06] Using read file: /corral4/main/objects/6/8/7/dataset_68771818-54a9-4b11-97b5-0a76985f5fd6.dat [10:16:06] Creating folder: 80012_S96_L001_R1_001_fastq [10:16:06] Changing working directory: 80012_S96_L001_R1_001_fastq [10:16:06] Creating reference folder: reference [10:16:06] Extracting FASTA and GFF from reference. Use of uninitialized value in uc at /usr/local/bin/snippy line 206, <GEN0> line 89. [10:16:06] Wrote 1 sequences to ref.fa [10:16:06] Wrote 0 features to ref.gff [10:16:06] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time. [10:16:06] Using BAM RG (Read Group) ID: 80012_S96_L001_R1_001_fastq [10:16:07] Running: samtools faidx reference/ref.fa 2>> snps.log [10:16:07] Error running command, check 80012_S96_L001_R1_001_fastq/snps.log
1[23:49:37] This is snippy 4.6.0
Show full stderr[23:49:37] This is snippy 4.6.0 [23:49:37] Written by Torsten Seemann [23:49:37] Obtained from https://github.com/tseemann/snippy [23:49:37] Detected operating system: linux [23:49:37] Enabling bundled linux tools. [23:49:37] Found bwa - /usr/local/bin/bwa [23:49:37] Found bcftools - /usr/local/bin/bcftools [23:49:37] Found samtools - /usr/local/bin/samtools [23:49:37] Found java - /usr/local/bin/java [23:49:37] Found snpEff - /usr/local/bin/snpEff [23:49:37] Found samclip - /usr/local/bin/samclip [23:49:37] Found seqtk - /usr/local/bin/seqtk [23:49:37] Found parallel - /usr/local/bin/parallel [23:49:37] Found freebayes - /usr/local/bin/freebayes [23:49:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [23:49:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [23:49:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [23:49:37] Found vcfuniq - /usr/local/bin/vcfuniq [23:49:37] Found vcffirstheader - /usr/local/bin/vcffirstheader [23:49:37] Found gzip - /bin/gzip [23:49:37] Found vt - /usr/local/bin/vt [23:49:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [23:49:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [23:49:38] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [23:49:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [23:49:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [23:49:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [23:49:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [23:49:39] Using reference: /corral4/main/objects/d/7/6/dataset_d764c547-d517-4ce6-9e7c-25fb605e00f7.dat [23:49:39] Treating reference as 'genbank' format. [23:49:39] Will use 1 CPU cores. [23:49:39] Using read file: /corral4/main/objects/c/7/1/dataset_c711a7bd-3ee2-4f67-a5fb-3c76fa60a96f.dat [23:49:39] Using read file: /corral4/main/objects/6/8/7/dataset_68771818-54a9-4b11-97b5-0a76985f5fd6.dat [23:49:39] Creating folder: 80012_S96_L001_R1_001_fastq [23:49:39] Changing working directory: 80012_S96_L001_R1_001_fastq [23:49:39] Creating reference folder: reference [23:49:39] Extracting FASTA and GFF from reference. Use of uninitialized value in uc at /usr/local/bin/snippy line 206, <GEN0> line 89. [23:49:39] Wrote 1 sequences to ref.fa [23:49:39] Wrote 0 features to ref.gff [23:49:39] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time. [23:49:39] Using BAM RG (Read Group) ID: 80012_S96_L001_R1_001_fastq [23:49:39] Running: samtools faidx reference/ref.fa 2>> snps.log [23:49:39] Error running command, check 80012_S96_L001_R1_001_fastq/snps.log
1[18:34:22] This is snippy 4.6.0
Show full stderr[18:34:22] This is snippy 4.6.0 [18:34:22] Written by Torsten Seemann [18:34:22] Obtained from https://github.com/tseemann/snippy [18:34:22] Detected operating system: linux [18:34:22] Enabling bundled linux tools. [18:34:22] Found bwa - /usr/local/bin/bwa [18:34:22] Found bcftools - /usr/local/bin/bcftools [18:34:22] Found samtools - /usr/local/bin/samtools [18:34:22] Found java - /usr/local/bin/java [18:34:22] Found snpEff - /usr/local/bin/snpEff [18:34:22] Found samclip - /usr/local/bin/samclip [18:34:22] Found seqtk - /usr/local/bin/seqtk [18:34:22] Found parallel - /usr/local/bin/parallel [18:34:22] Found freebayes - /usr/local/bin/freebayes [18:34:22] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [18:34:22] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [18:34:22] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [18:34:22] Found vcfuniq - /usr/local/bin/vcfuniq [18:34:22] Found vcffirstheader - /usr/local/bin/vcffirstheader [18:34:22] Found gzip - /bin/gzip [18:34:22] Found vt - /usr/local/bin/vt [18:34:22] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [18:34:22] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [18:34:22] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [18:34:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [18:34:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [18:34:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [18:34:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [18:34:23] Using reference: /cvmfs/data.galaxyproject.org/byhand/microbes/259/seq/eschColi_EDL933.fa [18:34:23] Treating reference as 'fasta' format. [18:34:23] Will use 1 CPU cores. [18:34:23] Using read file: /corral4/main/objects/1/c/f/dataset_1cfe77bd-7e11-44d6-9dce-84fc24f6e9ae.dat [18:34:23] Creating folder: Roary_on_dataset_27__39__and_others_Core_Gene_Alignment [18:34:23] Changing working directory: Roary_on_dataset_27__39__and_others_Core_Gene_Alignment [18:34:23] Creating reference folder: reference [18:34:23] Extracting FASTA and GFF from reference. [18:34:24] Wrote 2 sequences to ref.fa [18:34:24] Wrote 0 features to ref.gff [18:34:24] Shredding /corral4/main/objects/1/c/f/dataset_1cfe77bd-7e11-44d6-9dce-84fc24f6e9ae.dat into pseudo-reads [18:35:54] Wrote 8662850 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [18:35:54] Freebayes will process 1 chunks of 5714218 bp, 1 chunks at a time. [18:35:54] Using BAM RG (Read Group) ID: Roary_on_dataset_27__39__and_others_Core_Gene_Alignment [18:35:54] Running: samtools faidx reference/ref.fa 2>> snps.log [18:35:55] Running: bwa index reference/ref.fa 2>> snps.log [18:35:58] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [18:35:58] Running: ln -sf reference/ref.fa . 2>> snps.log [18:35:58] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [18:35:58] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [18:35:58] Running: bwa mem -Y -M -R '@RG\tID:Roary_on_dataset_27__39__and_others_Core_Gene_Alignment\tSM:Roary_on_dataset_27__39__and_others_Core_Gene_Alignment' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/951/72951307/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/951/72951307/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/951/72951307/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs
1[18:40:26] This is snippy 4.6.0
Show full stderr[18:40:26] This is snippy 4.6.0 [18:40:26] Written by Torsten Seemann [18:40:26] Obtained from https://github.com/tseemann/snippy [18:40:26] Detected operating system: linux [18:40:26] Enabling bundled linux tools. [18:40:26] Found bwa - /usr/local/bin/bwa [18:40:26] Found bcftools - /usr/local/bin/bcftools [18:40:26] Found samtools - /usr/local/bin/samtools [18:40:26] Found java - /usr/local/bin/java [18:40:26] Found snpEff - /usr/local/bin/snpEff [18:40:26] Found samclip - /usr/local/bin/samclip [18:40:26] Found seqtk - /usr/local/bin/seqtk [18:40:26] Found parallel - /usr/local/bin/parallel [18:40:26] Found freebayes - /usr/local/bin/freebayes [18:40:26] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [18:40:26] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [18:40:26] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [18:40:26] Found vcfuniq - /usr/local/bin/vcfuniq [18:40:26] Found vcffirstheader - /usr/local/bin/vcffirstheader [18:40:26] Found gzip - /bin/gzip [18:40:26] Found vt - /usr/local/bin/vt [18:40:26] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [18:40:26] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [18:40:26] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [18:40:26] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [18:40:26] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [18:40:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [18:40:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [18:40:27] Using reference: /cvmfs/data.galaxyproject.org/byhand/microbes/259/seq/eschColi_EDL933.fa [18:40:27] Treating reference as 'fasta' format. [18:40:27] Will use 1 CPU cores. [18:40:27] Using read file: /corral4/main/objects/1/c/f/dataset_1cfe77bd-7e11-44d6-9dce-84fc24f6e9ae.dat [18:40:27] Creating folder: Roary_on_dataset_27__39__and_others_Core_Gene_Alignment [18:40:27] Changing working directory: Roary_on_dataset_27__39__and_others_Core_Gene_Alignment [18:40:27] Creating reference folder: reference [18:40:27] Extracting FASTA and GFF from reference. [18:40:27] Wrote 2 sequences to ref.fa [18:40:27] Wrote 0 features to ref.gff [18:40:27] Shredding /corral4/main/objects/1/c/f/dataset_1cfe77bd-7e11-44d6-9dce-84fc24f6e9ae.dat into pseudo-reads [18:41:54] Wrote 8662850 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [18:41:54] Freebayes will process 1 chunks of 5714218 bp, 1 chunks at a time. [18:41:54] Using BAM RG (Read Group) ID: Roary_on_dataset_27__39__and_others_Core_Gene_Alignment [18:41:54] Running: samtools faidx reference/ref.fa 2>> snps.log [18:41:54] Running: bwa index reference/ref.fa 2>> snps.log [18:41:59] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [18:41:59] Running: ln -sf reference/ref.fa . 2>> snps.log [18:41:59] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [18:41:59] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [18:41:59] Running: bwa mem -Y -M -R '@RG\tID:Roary_on_dataset_27__39__and_others_Core_Gene_Alignment\tSM:Roary_on_dataset_27__39__and_others_Core_Gene_Alignment' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/951/72951382/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/951/72951382/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/951/72951382/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs
1[19:13:52] This is snippy 4.6.0
Show full stderr[19:13:52] This is snippy 4.6.0 [19:13:52] Written by Torsten Seemann [19:13:52] Obtained from https://github.com/tseemann/snippy [19:13:52] Detected operating system: linux [19:13:52] Enabling bundled linux tools. [19:13:52] Found bwa - /usr/local/bin/bwa [19:13:52] Found bcftools - /usr/local/bin/bcftools [19:13:52] Found samtools - /usr/local/bin/samtools [19:13:52] Found java - /usr/local/bin/java [19:13:52] Found snpEff - /usr/local/bin/snpEff [19:13:52] Found samclip - /usr/local/bin/samclip [19:13:52] Found seqtk - /usr/local/bin/seqtk [19:13:52] Found parallel - /usr/local/bin/parallel [19:13:52] Found freebayes - /usr/local/bin/freebayes [19:13:52] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [19:13:52] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [19:13:52] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [19:13:52] Found vcfuniq - /usr/local/bin/vcfuniq [19:13:52] Found vcffirstheader - /usr/local/bin/vcffirstheader [19:13:52] Found gzip - /bin/gzip [19:13:52] Found vt - /usr/local/bin/vt [19:13:52] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [19:13:52] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [19:13:52] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [19:13:52] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [19:13:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [19:13:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [19:13:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [19:13:54] Using reference: /cvmfs/data.galaxyproject.org/byhand/microbes/259/seq/eschColi_EDL933.fa [19:13:54] Treating reference as 'fasta' format. [19:13:54] Will use 1 CPU cores. [19:13:54] Using read file: /corral4/main/objects/1/c/f/dataset_1cfe77bd-7e11-44d6-9dce-84fc24f6e9ae.dat [19:13:54] Creating folder: Roary_on_dataset_27__39__and_others_Core_Gene_Alignment [19:13:54] Changing working directory: Roary_on_dataset_27__39__and_others_Core_Gene_Alignment [19:13:54] Creating reference folder: reference [19:13:54] Extracting FASTA and GFF from reference. [19:13:54] Wrote 2 sequences to ref.fa [19:13:54] Wrote 0 features to ref.gff [19:13:54] Shredding /corral4/main/objects/1/c/f/dataset_1cfe77bd-7e11-44d6-9dce-84fc24f6e9ae.dat into pseudo-reads [19:15:21] Wrote 8662850 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [19:15:21] Freebayes will process 1 chunks of 5714218 bp, 1 chunks at a time. [19:15:21] Using BAM RG (Read Group) ID: Roary_on_dataset_27__39__and_others_Core_Gene_Alignment [19:15:21] Running: samtools faidx reference/ref.fa 2>> snps.log [19:15:21] Running: bwa index reference/ref.fa 2>> snps.log [19:15:26] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [19:15:27] Running: ln -sf reference/ref.fa . 2>> snps.log [19:15:27] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [19:15:27] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [19:15:27] Running: bwa mem -Y -M -R '@RG\tID:Roary_on_dataset_27__39__and_others_Core_Gene_Alignment\tSM:Roary_on_dataset_27__39__and_others_Core_Gene_Alignment' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/951/72951996/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/951/72951996/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/951/72951996/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs
1[19:21:23] This is snippy 4.6.0
Show full stderr[19:21:23] This is snippy 4.6.0 [19:21:23] Written by Torsten Seemann [19:21:23] Obtained from https://github.com/tseemann/snippy [19:21:23] Detected operating system: linux [19:21:23] Enabling bundled linux tools. [19:21:23] Found bwa - /usr/local/bin/bwa [19:21:23] Found bcftools - /usr/local/bin/bcftools [19:21:23] Found samtools - /usr/local/bin/samtools [19:21:23] Found java - /usr/local/bin/java [19:21:23] Found snpEff - /usr/local/bin/snpEff [19:21:23] Found samclip - /usr/local/bin/samclip [19:21:23] Found seqtk - /usr/local/bin/seqtk [19:21:23] Found parallel - /usr/local/bin/parallel [19:21:23] Found freebayes - /usr/local/bin/freebayes [19:21:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [19:21:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [19:21:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [19:21:23] Found vcfuniq - /usr/local/bin/vcfuniq [19:21:23] Found vcffirstheader - /usr/local/bin/vcffirstheader [19:21:23] Found gzip - /bin/gzip [19:21:23] Found vt - /usr/local/bin/vt [19:21:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [19:21:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [19:21:23] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [19:21:24] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [19:21:24] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [19:21:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [19:21:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [19:21:24] Using reference: /cvmfs/data.galaxyproject.org/byhand/microbes/259/seq/eschColi_EDL933.fa [19:21:24] Treating reference as 'fasta' format. [19:21:24] Will use 1 CPU cores. [19:21:24] Using read file: /corral4/main/objects/1/c/f/dataset_1cfe77bd-7e11-44d6-9dce-84fc24f6e9ae.dat [19:21:24] Creating folder: Roary_on_dataset_27__39__and_others_Core_Gene_Alignment [19:21:24] Changing working directory: Roary_on_dataset_27__39__and_others_Core_Gene_Alignment [19:21:24] Creating reference folder: reference [19:21:24] Extracting FASTA and GFF from reference. [19:21:25] Wrote 2 sequences to ref.fa [19:21:25] Wrote 0 features to ref.gff [19:21:25] Shredding /corral4/main/objects/1/c/f/dataset_1cfe77bd-7e11-44d6-9dce-84fc24f6e9ae.dat into pseudo-reads [19:22:50] Wrote 8662850 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [19:22:50] Freebayes will process 1 chunks of 5714218 bp, 1 chunks at a time. [19:22:50] Using BAM RG (Read Group) ID: Roary_on_dataset_27__39__and_others_Core_Gene_Alignment [19:22:50] Running: samtools faidx reference/ref.fa 2>> snps.log [19:22:50] Running: bwa index reference/ref.fa 2>> snps.log [19:22:55] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [19:22:55] Running: ln -sf reference/ref.fa . 2>> snps.log [19:22:55] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [19:22:55] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [19:22:55] Running: bwa mem -Y -M -R '@RG\tID:Roary_on_dataset_27__39__and_others_Core_Gene_Alignment\tSM:Roary_on_dataset_27__39__and_others_Core_Gene_Alignment' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/952/72952095/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/952/72952095/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/952/72952095/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs
1[20:37:58] This is snippy 4.6.0
Show full stderr[20:37:58] This is snippy 4.6.0 [20:37:58] Written by Torsten Seemann [20:37:58] Obtained from https://github.com/tseemann/snippy [20:37:58] Detected operating system: linux [20:37:58] Enabling bundled linux tools. [20:37:58] Found bwa - /usr/local/bin/bwa [20:37:58] Found bcftools - /usr/local/bin/bcftools [20:37:58] Found samtools - /usr/local/bin/samtools [20:37:58] Found java - /usr/local/bin/java [20:37:58] Found snpEff - /usr/local/bin/snpEff [20:37:58] Found samclip - /usr/local/bin/samclip [20:37:58] Found seqtk - /usr/local/bin/seqtk [20:37:58] Found parallel - /usr/local/bin/parallel [20:37:58] Found freebayes - /usr/local/bin/freebayes [20:37:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [20:37:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [20:37:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [20:37:58] Found vcfuniq - /usr/local/bin/vcfuniq [20:37:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [20:37:58] Found gzip - /bin/gzip [20:37:58] Found vt - /usr/local/bin/vt [20:37:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [20:37:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [20:37:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [20:37:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [20:37:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [20:37:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [20:37:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [20:37:59] Using reference: /cvmfs/data.galaxyproject.org/byhand/microbes/259/seq/eschColi_EDL933.fa [20:37:59] Treating reference as 'fasta' format. [20:37:59] Will use 1 CPU cores. [20:37:59] Using read file: /corral4/main/objects/1/c/f/dataset_1cfe77bd-7e11-44d6-9dce-84fc24f6e9ae.dat [20:37:59] Creating folder: Roary_on_dataset_27__39__and_others_Core_Gene_Alignment [20:37:59] Changing working directory: Roary_on_dataset_27__39__and_others_Core_Gene_Alignment [20:37:59] Creating reference folder: reference [20:37:59] Extracting FASTA and GFF from reference. [20:37:59] Wrote 2 sequences to ref.fa [20:37:59] Wrote 0 features to ref.gff [20:37:59] Shredding /corral4/main/objects/1/c/f/dataset_1cfe77bd-7e11-44d6-9dce-84fc24f6e9ae.dat into pseudo-reads [20:39:29] Wrote 8662850 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [20:39:29] Freebayes will process 1 chunks of 5714218 bp, 1 chunks at a time. [20:39:29] Using BAM RG (Read Group) ID: Roary_on_dataset_27__39__and_others_Core_Gene_Alignment [20:39:29] Running: samtools faidx reference/ref.fa 2>> snps.log [20:39:30] Running: bwa index reference/ref.fa 2>> snps.log [20:39:35] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [20:39:35] Running: ln -sf reference/ref.fa . 2>> snps.log [20:39:35] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [20:39:35] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [20:39:35] Running: bwa mem -Y -M -R '@RG\tID:Roary_on_dataset_27__39__and_others_Core_Gene_Alignment\tSM:Roary_on_dataset_27__39__and_others_Core_Gene_Alignment' -t 1 reference/ref.fa fake_reads.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/072/953/72953104/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/072/953/72953104/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/072/953/72953104/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs
1[10:36:35] This is snippy 4.6.0
Show full stderr[10:36:35] This is snippy 4.6.0 [10:36:35] Written by Torsten Seemann [10:36:35] Obtained from https://github.com/tseemann/snippy [10:36:35] Detected operating system: linux [10:36:35] Enabling bundled linux tools. [10:36:35] Found bwa - /usr/local/bin/bwa [10:36:35] Found bcftools - /usr/local/bin/bcftools [10:36:35] Found samtools - /usr/local/bin/samtools [10:36:35] Found java - /usr/local/bin/java [10:36:35] Found snpEff - /usr/local/bin/snpEff [10:36:35] Found samclip - /usr/local/bin/samclip [10:36:35] Found seqtk - /usr/local/bin/seqtk [10:36:35] Found parallel - /usr/local/bin/parallel [10:36:35] Found freebayes - /usr/local/bin/freebayes [10:36:35] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [10:36:35] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [10:36:35] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [10:36:35] Found vcfuniq - /usr/local/bin/vcfuniq [10:36:35] Found vcffirstheader - /usr/local/bin/vcffirstheader [10:36:35] Found gzip - /bin/gzip [10:36:35] Found vt - /usr/local/bin/vt [10:36:35] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [10:36:35] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [10:36:35] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [10:36:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [10:36:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [10:36:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [10:36:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [10:36:36] Using reference: /corral4/main/objects/a/e/9/dataset_ae9a2554-5d57-4553-ade6-30f5f7661efb.dat [10:36:36] Treating reference as 'genbank' format. [10:36:36] Will use 1 CPU cores. [10:36:36] Using read file: /corral4/main/objects/a/0/c/dataset_a0cf1cb7-6df7-4707-83f4-1818a17e2077.dat [10:36:36] Using read file: /corral4/main/objects/b/c/3/dataset_bc3e9a48-3624-4dbc-bae0-7446ba54eae1.dat [10:36:36] Creating folder: SRR10761128 [10:36:36] Changing working directory: SRR10761128 [10:36:36] Creating reference folder: reference [10:36:36] Extracting FASTA and GFF from reference. [10:36:39] Wrote 1 sequences to ref.fa [10:36:39] Wrote 4497 features to ref.gff [10:36:39] Creating reference/snpeff.config [10:36:39] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time. [10:36:39] Using BAM RG (Read Group) ID: SRR10761128 [10:36:39] Running: samtools faidx reference/ref.fa 2>> snps.log [10:36:39] Error running command, check SRR10761128/snps.log
1[10:39:03] This is snippy 4.6.0
Show full stderr[10:39:03] This is snippy 4.6.0 [10:39:03] Written by Torsten Seemann [10:39:03] Obtained from https://github.com/tseemann/snippy [10:39:03] Detected operating system: linux [10:39:03] Enabling bundled linux tools. [10:39:03] Found bwa - /usr/local/bin/bwa [10:39:03] Found bcftools - /usr/local/bin/bcftools [10:39:03] Found samtools - /usr/local/bin/samtools [10:39:03] Found java - /usr/local/bin/java [10:39:03] Found snpEff - /usr/local/bin/snpEff [10:39:03] Found samclip - /usr/local/bin/samclip [10:39:03] Found seqtk - /usr/local/bin/seqtk [10:39:03] Found parallel - /usr/local/bin/parallel [10:39:03] Found freebayes - /usr/local/bin/freebayes [10:39:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [10:39:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [10:39:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [10:39:04] Found vcfuniq - /usr/local/bin/vcfuniq [10:39:04] Found vcffirstheader - /usr/local/bin/vcffirstheader [10:39:04] Found gzip - /bin/gzip [10:39:04] Found vt - /usr/local/bin/vt [10:39:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [10:39:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [10:39:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [10:39:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [10:39:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [10:39:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [10:39:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [10:39:04] Using reference: /corral4/main/objects/a/e/9/dataset_ae9a2554-5d57-4553-ade6-30f5f7661efb.dat [10:39:05] Treating reference as 'genbank' format. [10:39:05] Will use 1 CPU cores. [10:39:05] Using read file: /corral4/main/objects/e/b/c/dataset_ebcda2c4-64a4-4237-99cd-cc85eef2d369.dat [10:39:05] Using read file: /corral4/main/objects/d/f/f/dataset_dffb6778-0efb-4c92-be32-92f376eb578a.dat [10:39:05] Creating folder: SRR10761127 [10:39:05] Changing working directory: SRR10761127 [10:39:05] Creating reference folder: reference [10:39:05] Extracting FASTA and GFF from reference. [10:39:07] Wrote 1 sequences to ref.fa [10:39:07] Wrote 4497 features to ref.gff [10:39:07] Creating reference/snpeff.config [10:39:07] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time. [10:39:07] Using BAM RG (Read Group) ID: SRR10761127 [10:39:07] Running: samtools faidx reference/ref.fa 2>> snps.log [10:39:07] Error running command, check SRR10761127/snps.log
1[10:40:54] This is snippy 4.6.0
Show full stderr[10:40:54] This is snippy 4.6.0 [10:40:54] Written by Torsten Seemann [10:40:54] Obtained from https://github.com/tseemann/snippy [10:40:54] Detected operating system: linux [10:40:54] Enabling bundled linux tools. [10:40:54] Found bwa - /usr/local/bin/bwa [10:40:54] Found bcftools - /usr/local/bin/bcftools [10:40:55] Found samtools - /usr/local/bin/samtools [10:40:55] Found java - /usr/local/bin/java [10:40:55] Found snpEff - /usr/local/bin/snpEff [10:40:55] Found samclip - /usr/local/bin/samclip [10:40:55] Found seqtk - /usr/local/bin/seqtk [10:40:55] Found parallel - /usr/local/bin/parallel [10:40:55] Found freebayes - /usr/local/bin/freebayes [10:40:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [10:40:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [10:40:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [10:40:55] Found vcfuniq - /usr/local/bin/vcfuniq [10:40:55] Found vcffirstheader - /usr/local/bin/vcffirstheader [10:40:55] Found gzip - /bin/gzip [10:40:55] Found vt - /usr/local/bin/vt [10:40:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [10:40:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [10:40:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [10:40:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [10:40:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [10:40:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [10:40:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [10:40:55] Using reference: /corral4/main/objects/a/e/9/dataset_ae9a2554-5d57-4553-ade6-30f5f7661efb.dat [10:40:56] Treating reference as 'genbank' format. [10:40:56] Will use 1 CPU cores. [10:40:56] Using read file: /corral4/main/objects/c/5/6/dataset_c56e56b0-69e2-4905-bb28-d1a0854f51e4.dat [10:40:56] Using read file: /corral4/main/objects/9/2/2/dataset_922c6e30-956d-4c2d-bc51-8cc2d5668c34.dat [10:40:56] Creating folder: SRR10761126 [10:40:56] Changing working directory: SRR10761126 [10:40:56] Creating reference folder: reference [10:40:56] Extracting FASTA and GFF from reference. [10:40:58] Wrote 1 sequences to ref.fa [10:40:58] Wrote 4497 features to ref.gff [10:40:58] Creating reference/snpeff.config [10:40:58] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time. [10:40:58] Using BAM RG (Read Group) ID: SRR10761126 [10:40:58] Running: samtools faidx reference/ref.fa 2>> snps.log [10:40:58] Error running command, check SRR10761126/snps.log
1[10:50:21] This is snippy 4.6.0
Show full stderr[10:50:21] This is snippy 4.6.0 [10:50:21] Written by Torsten Seemann [10:50:21] Obtained from https://github.com/tseemann/snippy [10:50:21] Detected operating system: linux [10:50:21] Enabling bundled linux tools. [10:50:21] Found bwa - /usr/local/bin/bwa [10:50:21] Found bcftools - /usr/local/bin/bcftools [10:50:21] Found samtools - /usr/local/bin/samtools [10:50:21] Found java - /usr/local/bin/java [10:50:21] Found snpEff - /usr/local/bin/snpEff [10:50:21] Found samclip - /usr/local/bin/samclip [10:50:21] Found seqtk - /usr/local/bin/seqtk [10:50:21] Found parallel - /usr/local/bin/parallel [10:50:21] Found freebayes - /usr/local/bin/freebayes [10:50:21] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [10:50:21] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [10:50:21] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [10:50:21] Found vcfuniq - /usr/local/bin/vcfuniq [10:50:21] Found vcffirstheader - /usr/local/bin/vcffirstheader [10:50:21] Found gzip - /bin/gzip [10:50:21] Found vt - /usr/local/bin/vt [10:50:21] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [10:50:21] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [10:50:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [10:50:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [10:50:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [10:50:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [10:50:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [10:50:22] Using reference: /corral4/main/objects/a/e/9/dataset_ae9a2554-5d57-4553-ade6-30f5f7661efb.dat [10:50:22] Treating reference as 'genbank' format. [10:50:22] Will use 1 CPU cores. [10:50:22] Using read file: /corral4/main/objects/c/5/6/dataset_c56e56b0-69e2-4905-bb28-d1a0854f51e4.dat [10:50:22] Using read file: /corral4/main/objects/9/2/2/dataset_922c6e30-956d-4c2d-bc51-8cc2d5668c34.dat [10:50:22] Creating folder: SRR10761126_forward [10:50:22] Changing working directory: SRR10761126_forward [10:50:22] Creating reference folder: reference [10:50:22] Extracting FASTA and GFF from reference. [10:50:24] Wrote 1 sequences to ref.fa [10:50:24] Wrote 4497 features to ref.gff [10:50:24] Creating reference/snpeff.config [10:50:24] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time. [10:50:24] Using BAM RG (Read Group) ID: SRR10761126_forward [10:50:25] Running: samtools faidx reference/ref.fa 2>> snps.log [10:50:25] Error running command, check SRR10761126_forward/snps.log
1[05:01:54] This is snippy 4.6.0
Show full stderr[05:01:54] This is snippy 4.6.0 [05:01:54] Written by Torsten Seemann [05:01:54] Obtained from https://github.com/tseemann/snippy [05:01:54] Detected operating system: linux [05:01:54] Enabling bundled linux tools. [05:01:54] Found bwa - /usr/local/bin/bwa [05:01:54] Found bcftools - /usr/local/bin/bcftools [05:01:54] Found samtools - /usr/local/bin/samtools [05:01:54] Found java - /usr/local/bin/java [05:01:54] Found snpEff - /usr/local/bin/snpEff [05:01:54] Found samclip - /usr/local/bin/samclip [05:01:54] Found seqtk - /usr/local/bin/seqtk [05:01:54] Found parallel - /usr/local/bin/parallel [05:01:54] Found freebayes - /usr/local/bin/freebayes [05:01:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:01:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:01:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:01:54] Found vcfuniq - /usr/local/bin/vcfuniq [05:01:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:01:54] Found gzip - /bin/gzip [05:01:54] Found vt - /usr/local/bin/vt [05:01:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:01:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:01:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:01:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:01:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:01:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:01:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:01:58] Using reference: /corral4/main/objects/7/5/7/dataset_7577fd1d-8b44-4cce-a677-6380b78479e2.dat [05:01:58] Treating reference as 'fasta' format. [05:01:58] Will use 1 CPU cores. [05:01:58] Using read file: /corral4/main/objects/8/c/2/dataset_8c2be7c9-ec84-4b97-9200-90b4f1ca87cb.dat [05:01:58] Using read file: /corral4/main/objects/4/e/8/dataset_4e87b4ce-e697-4bfd-acd0-b02bfb0ac039.dat [05:01:58] Creating folder: S7_R1_fastq_gz [05:01:58] Changing working directory: S7_R1_fastq_gz [05:01:58] Creating reference folder: reference [05:01:58] Extracting FASTA and GFF from reference. [05:01:58] Wrote 15 sequences to ref.fa [05:01:58] Wrote 0 features to ref.gff [05:01:58] Freebayes will process 1 chunks of 12573413 bp, 1 chunks at a time. [05:01:58] Using BAM RG (Read Group) ID: S7_R1_fastq_gz [05:01:58] Running: samtools faidx reference/ref.fa 2>> snps.log [05:01:59] Running: bwa index reference/ref.fa 2>> snps.log [05:02:08] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [05:02:08] Running: ln -sf reference/ref.fa . 2>> snps.log [05:02:08] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [05:02:08] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [05:02:08] Running: bwa mem -Y -M -R '@RG\tID:S7_R1_fastq_gz\tSM:S7_R1_fastq_gz' -t 1 reference/ref.fa /corral4/main/objects/8/c/2/dataset_8c2be7c9-ec84-4b97-9200-90b4f1ca87cb.dat /corral4/main/objects/4/e/8/dataset_4e87b4ce-e697-4bfd-acd0-b02bfb0ac039.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/073/010/73010224/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/073/010/73010224/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/073/010/73010224/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 15 sequences in reference/
1[08:54:49] This is snippy 4.6.0
Show full stderr[08:54:49] This is snippy 4.6.0 [08:54:49] Written by Torsten Seemann [08:54:49] Obtained from https://github.com/tseemann/snippy [08:54:49] Detected operating system: linux [08:54:49] Enabling bundled linux tools. [08:54:49] Found bwa - /usr/local/bin/bwa [08:54:49] Found bcftools - /usr/local/bin/bcftools [08:54:49] Found samtools - /usr/local/bin/samtools [08:54:49] Found java - /usr/local/bin/java [08:54:49] Found snpEff - /usr/local/bin/snpEff [08:54:49] Found samclip - /usr/local/bin/samclip [08:54:49] Found seqtk - /usr/local/bin/seqtk [08:54:49] Found parallel - /usr/local/bin/parallel [08:54:49] Found freebayes - /usr/local/bin/freebayes [08:54:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:54:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:54:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:54:49] Found vcfuniq - /usr/local/bin/vcfuniq [08:54:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:54:49] Found gzip - /bin/gzip [08:54:49] Found vt - /usr/local/bin/vt [08:54:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:54:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:54:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:54:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:54:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:54:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:54:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:54:50] Using reference: /corral4/main/objects/6/7/d/dataset_67dc2d8d-ac2c-40ad-98bd-47ceff4d01ae.dat [08:54:50] Treating reference as 'genbank' format. [08:54:50] Will use 1 CPU cores. [08:54:50] Using read file: /corral4/main/objects/d/8/e/dataset_d8ebdec0-6eff-408f-be70-4806857fadcf.dat [08:54:50] Creating folder: PAK_resistant_Strain_zip [08:54:50] Changing working directory: PAK_resistant_Strain_zip [08:54:50] Creating reference folder: reference [08:54:50] Extracting FASTA and GFF from reference. [08:54:53] Wrote 1 sequences to ref.fa [08:54:53] Wrote 5867 features to ref.gff [08:54:53] Creating reference/snpeff.config [08:54:53] Freebayes will process 1 chunks of 6502546 bp, 1 chunks at a time. [08:54:53] Using BAM RG (Read Group) ID: PAK_resistant_Strain_zip [08:54:53] Running: samtools faidx reference/ref.fa 2>> snps.log [08:54:53] Running: bwa index reference/ref.fa 2>> snps.log [08:54:57] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [08:54:58] Running: ln -sf reference/ref.fa . 2>> snps.log [08:54:58] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [08:54:58] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [08:54:58] Running: snpEff build -c reference/snpeff.config -dataDir . -gff3 ref 2>> snps.log [08:55:04] Running: bwa mem -Y -M -R '@RG\tID:PAK_resistant_Strain_zip\tSM:PAK_resistant_Strain_zip' -t 1 reference/ref.fa /corral4/main/objects/d/8/e/dataset_d8ebdec0-6eff-408f-be70-4806857fadcf.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/073/013/73013861/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/073/013/73013861/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/073/013/73013861/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 1 sequences
1[08:54:58] This is snippy 4.6.0
Show full stderr[08:54:58] This is snippy 4.6.0 [08:54:58] Written by Torsten Seemann [08:54:58] Obtained from https://github.com/tseemann/snippy [08:54:58] Detected operating system: linux [08:54:58] Enabling bundled linux tools. [08:54:58] Found bwa - /usr/local/bin/bwa [08:54:58] Found bcftools - /usr/local/bin/bcftools [08:54:58] Found samtools - /usr/local/bin/samtools [08:54:58] Found java - /usr/local/bin/java [08:54:58] Found snpEff - /usr/local/bin/snpEff [08:54:58] Found samclip - /usr/local/bin/samclip [08:54:58] Found seqtk - /usr/local/bin/seqtk [08:54:58] Found parallel - /usr/local/bin/parallel [08:54:58] Found freebayes - /usr/local/bin/freebayes [08:54:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:54:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:54:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:54:58] Found vcfuniq - /usr/local/bin/vcfuniq [08:54:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:54:58] Found gzip - /bin/gzip [08:54:58] Found vt - /usr/local/bin/vt [08:54:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:54:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:54:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:54:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:54:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:54:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:54:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:54:59] Using reference: /corral4/main/objects/c/c/c/dataset_ccc76921-13cc-409b-ab75-a966e36a5169.dat [08:54:59] Treating reference as 'genbank' format. [08:54:59] Will use 1 CPU cores. [08:54:59] Using read file: /corral4/main/objects/a/e/0/dataset_ae0fae57-731f-4dbf-9965-c646cbb4af08.dat [08:54:59] Creating folder: PAK_resistant_Strain_zip [08:54:59] Changing working directory: PAK_resistant_Strain_zip [08:54:59] Creating reference folder: reference [08:54:59] Extracting FASTA and GFF from reference. [08:55:02] Wrote 1 sequences to ref.fa [08:55:02] Wrote 5867 features to ref.gff [08:55:02] Creating reference/snpeff.config [08:55:02] Freebayes will process 1 chunks of 6502546 bp, 1 chunks at a time. [08:55:02] Using BAM RG (Read Group) ID: PAK_resistant_Strain_zip [08:55:02] Running: samtools faidx reference/ref.fa 2>> snps.log [08:55:02] Running: bwa index reference/ref.fa 2>> snps.log [08:55:06] Error running command, check PAK_resistant_Strain_zip/snps.log
1[08:55:10] This is snippy 4.6.0
Show full stderr[08:55:10] This is snippy 4.6.0 [08:55:10] Written by Torsten Seemann [08:55:10] Obtained from https://github.com/tseemann/snippy [08:55:10] Detected operating system: linux [08:55:10] Enabling bundled linux tools. [08:55:10] Found bwa - /usr/local/bin/bwa [08:55:10] Found bcftools - /usr/local/bin/bcftools [08:55:10] Found samtools - /usr/local/bin/samtools [08:55:10] Found java - /usr/local/bin/java [08:55:10] Found snpEff - /usr/local/bin/snpEff [08:55:10] Found samclip - /usr/local/bin/samclip [08:55:10] Found seqtk - /usr/local/bin/seqtk [08:55:10] Found parallel - /usr/local/bin/parallel [08:55:10] Found freebayes - /usr/local/bin/freebayes [08:55:10] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:55:10] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:55:10] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:55:11] Found vcfuniq - /usr/local/bin/vcfuniq [08:55:11] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:55:11] Found gzip - /bin/gzip [08:55:11] Found vt - /usr/local/bin/vt [08:55:11] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:55:11] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:55:11] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:55:11] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:55:11] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:55:12] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:55:12] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:55:12] Using reference: /corral4/main/objects/7/f/1/dataset_7f1bab6e-e981-4cc0-bed7-4a7086b7b340.dat [08:55:14] Treating reference as 'genbank' format. [08:55:14] Will use 1 CPU cores. [08:55:15] Using read file: /corral4/main/objects/f/b/a/dataset_fbac96ca-2c12-45fd-b918-1f649020b6af.dat [08:55:15] Creating folder: PAK_resistant_Strain_zip [08:55:15] Changing working directory: PAK_resistant_Strain_zip [08:55:15] Creating reference folder: reference [08:55:15] Extracting FASTA and GFF from reference. [08:55:18] Wrote 1 sequences to ref.fa [08:55:18] Wrote 5867 features to ref.gff [08:55:18] Creating reference/snpeff.config [08:55:19] Freebayes will process 1 chunks of 6502546 bp, 1 chunks at a time. [08:55:19] Using BAM RG (Read Group) ID: PAK_resistant_Strain_zip [08:55:19] Running: samtools faidx reference/ref.fa 2>> snps.log [08:55:20] Running: bwa index reference/ref.fa 2>> snps.log [08:55:28] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [08:55:28] Running: ln -sf reference/ref.fa . 2>> snps.log [08:55:28] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [08:55:29] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [08:55:30] Running: snpEff build -c reference/snpeff.config -dataDir . -gff3 ref 2>> snps.log [08:55:37] Running: bwa mem -Y -M -R '@RG\tID:PAK_resistant_Strain_zip\tSM:PAK_resistant_Strain_zip' -t 1 reference/ref.fa /corral4/main/objects/f/b/a/dataset_fbac96ca-2c12-45fd-b918-1f649020b6af.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/073/013/73013871/tmp --threads 0 -m 4000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/073/013/73013871/tmp --threads 0 -m 4000M | samtools markdup -T /corral4/main/jobs/073/013/73013871/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 1 sequences in reference/ref.fa.fai [M::bwa_idx_load_from_disk
1[08:55:03] This is snippy 4.6.0
Show full stderr[08:55:03] This is snippy 4.6.0 [08:55:03] Written by Torsten Seemann [08:55:03] Obtained from https://github.com/tseemann/snippy [08:55:03] Detected operating system: linux [08:55:03] Enabling bundled linux tools. [08:55:04] Found bwa - /usr/local/bin/bwa [08:55:04] Found bcftools - /usr/local/bin/bcftools [08:55:04] Found samtools - /usr/local/bin/samtools [08:55:04] Found java - /usr/local/bin/java [08:55:04] Found snpEff - /usr/local/bin/snpEff [08:55:04] Found samclip - /usr/local/bin/samclip [08:55:04] Found seqtk - /usr/local/bin/seqtk [08:55:04] Found parallel - /usr/local/bin/parallel [08:55:04] Found freebayes - /usr/local/bin/freebayes [08:55:04] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:55:04] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:55:04] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:55:04] Found vcfuniq - /usr/local/bin/vcfuniq [08:55:04] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:55:04] Found gzip - /bin/gzip [08:55:04] Found vt - /usr/local/bin/vt [08:55:04] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:55:04] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:55:04] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:55:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:55:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:55:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:55:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:55:04] Using reference: /corral4/main/objects/4/a/f/dataset_4af21818-52fd-41ed-b756-3780f3f34fd3.dat [08:55:04] Treating reference as 'genbank' format. [08:55:04] Will use 1 CPU cores. [08:55:05] Using read file: /corral4/main/objects/3/1/3/dataset_3133fc9f-f54e-447d-8f0e-2b980a1bc605.dat [08:55:05] Creating folder: PAK_resistant_Strain_zip [08:55:05] Changing working directory: PAK_resistant_Strain_zip [08:55:05] Creating reference folder: reference [08:55:05] Extracting FASTA and GFF from reference. [08:55:08] Wrote 1 sequences to ref.fa [08:55:08] Wrote 5867 features to ref.gff [08:55:08] Creating reference/snpeff.config [08:55:08] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time. [08:55:08] Using BAM RG (Read Group) ID: PAK_resistant_Strain_zip [08:55:08] Running: samtools faidx reference/ref.fa 2>> snps.log [08:55:08] Error running command, check PAK_resistant_Strain_zip/snps.log
1[08:55:07] This is snippy 4.6.0
Show full stderr[08:55:07] This is snippy 4.6.0 [08:55:07] Written by Torsten Seemann [08:55:07] Obtained from https://github.com/tseemann/snippy [08:55:07] Detected operating system: linux [08:55:07] Enabling bundled linux tools. [08:55:07] Found bwa - /usr/local/bin/bwa [08:55:07] Found bcftools - /usr/local/bin/bcftools [08:55:07] Found samtools - /usr/local/bin/samtools [08:55:07] Found java - /usr/local/bin/java [08:55:07] Found snpEff - /usr/local/bin/snpEff [08:55:07] Found samclip - /usr/local/bin/samclip [08:55:07] Found seqtk - /usr/local/bin/seqtk [08:55:07] Found parallel - /usr/local/bin/parallel [08:55:07] Found freebayes - /usr/local/bin/freebayes [08:55:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:55:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:55:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:55:07] Found vcfuniq - /usr/local/bin/vcfuniq [08:55:07] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:55:07] Found gzip - /bin/gzip [08:55:07] Found vt - /usr/local/bin/vt [08:55:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:55:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:55:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:55:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:55:07] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:55:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:55:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:55:07] Using reference: /corral4/main/objects/5/2/1/dataset_52175a55-fab0-4a59-828e-1ca4a8985152.dat [08:55:08] Treating reference as 'genbank' format. [08:55:08] Will use 1 CPU cores. [08:55:08] Using read file: /corral4/main/objects/a/d/b/dataset_adb62186-f480-4f52-b6fd-20b5c72713cd.dat [08:55:08] Using read file: /corral4/main/objects/a/d/b/dataset_adb62186-f480-4f52-b6fd-20b5c72713cd.dat [08:55:08] Creating folder: Pseudomonas_aeruginosa_PAK_genomic_fasta [08:55:08] Changing working directory: Pseudomonas_aeruginosa_PAK_genomic_fasta [08:55:08] Creating reference folder: reference [08:55:08] Extracting FASTA and GFF from reference. [08:55:11] Wrote 1 sequences to ref.fa [08:55:11] Wrote 5867 features to ref.gff [08:55:11] Creating reference/snpeff.config [08:55:11] Freebayes will process 1 chunks of 6502546 bp, 1 chunks at a time. [08:55:11] Using BAM RG (Read Group) ID: Pseudomonas_aeruginosa_PAK_genomic_fasta [08:55:11] Running: samtools faidx reference/ref.fa 2>> snps.log [08:55:11] Error running command, check Pseudomonas_aeruginosa_PAK_genomic_fasta/snps.log
1[08:55:13] This is snippy 4.6.0
Show full stderr[08:55:13] This is snippy 4.6.0 [08:55:13] Written by Torsten Seemann [08:55:13] Obtained from https://github.com/tseemann/snippy [08:55:13] Detected operating system: linux [08:55:13] Enabling bundled linux tools. [08:55:13] Found bwa - /usr/local/bin/bwa [08:55:13] Found bcftools - /usr/local/bin/bcftools [08:55:13] Found samtools - /usr/local/bin/samtools [08:55:13] Found java - /usr/local/bin/java [08:55:13] Found snpEff - /usr/local/bin/snpEff [08:55:13] Found samclip - /usr/local/bin/samclip [08:55:13] Found seqtk - /usr/local/bin/seqtk [08:55:13] Found parallel - /usr/local/bin/parallel [08:55:13] Found freebayes - /usr/local/bin/freebayes [08:55:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:55:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:55:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:55:14] Found vcfuniq - /usr/local/bin/vcfuniq [08:55:14] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:55:14] Found gzip - /bin/gzip [08:55:14] Found vt - /usr/local/bin/vt [08:55:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:55:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:55:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:55:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:55:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:55:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:55:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:55:15] Using reference: /corral4/main/objects/8/2/d/dataset_82d0c8e3-2375-41f8-859c-34b1990f6893.dat [08:55:18] Treating reference as 'genbank' format. [08:55:18] Will use 1 CPU cores. [08:55:18] Using read file: /corral4/main/objects/f/0/8/dataset_f0833e1f-e880-4a4f-83dc-b658e7b8831a.dat [08:55:18] --tmpdir '/corral4/main/jobs/073/013/73013875/tmp' is not a directory
1[08:55:39] This is snippy 4.6.0
Show full stderr[08:55:39] This is snippy 4.6.0 [08:55:39] Written by Torsten Seemann [08:55:39] Obtained from https://github.com/tseemann/snippy [08:55:39] Detected operating system: linux [08:55:39] Enabling bundled linux tools. [08:55:39] Found bwa - /usr/local/bin/bwa [08:55:39] Found bcftools - /usr/local/bin/bcftools [08:55:39] Found samtools - /usr/local/bin/samtools [08:55:39] Found java - /usr/local/bin/java [08:55:39] Found snpEff - /usr/local/bin/snpEff [08:55:39] Found samclip - /usr/local/bin/samclip [08:55:39] Found seqtk - /usr/local/bin/seqtk [08:55:39] Found parallel - /usr/local/bin/parallel [08:55:39] Found freebayes - /usr/local/bin/freebayes [08:55:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:55:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:55:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:55:39] Found vcfuniq - /usr/local/bin/vcfuniq [08:55:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:55:39] Found gzip - /bin/gzip [08:55:39] Found vt - /usr/local/bin/vt [08:55:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:55:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:55:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:55:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:55:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:55:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:55:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:55:39] Using reference: /corral4/main/objects/5/0/5/dataset_505c5c07-39f6-4728-92bc-03c4683bad52.dat [08:55:40] Treating reference as 'genbank' format. [08:55:40] Will use 1 CPU cores. [08:55:40] Using read file: /corral4/main/objects/7/0/5/dataset_7059f343-4fa8-4e05-be77-28232f0efe0a.dat [08:55:40] Creating folder: PAK_resistant_Strain_zip [08:55:40] Changing working directory: PAK_resistant_Strain_zip [08:55:40] Creating reference folder: reference [08:55:40] Extracting FASTA and GFF from reference. [08:55:43] Wrote 1 sequences to ref.fa [08:55:43] Wrote 5867 features to ref.gff [08:55:43] Creating reference/snpeff.config [08:55:43] Freebayes will process 1 chunks of 6502546 bp, 1 chunks at a time. [08:55:43] Using BAM RG (Read Group) ID: PAK_resistant_Strain_zip [08:55:43] Running: samtools faidx reference/ref.fa 2>> snps.log [08:55:43] Running: bwa index reference/ref.fa 2>> snps.log [08:55:47] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [08:55:47] Running: ln -sf reference/ref.fa . 2>> snps.log [08:55:47] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [08:55:47] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [08:55:47] Running: snpEff build -c reference/snpeff.config -dataDir . -gff3 ref 2>> snps.log [08:55:53] Running: bwa mem -Y -M -R '@RG\tID:PAK_resistant_Strain_zip\tSM:PAK_resistant_Strain_zip' -t 1 reference/ref.fa /corral4/main/objects/7/0/5/dataset_7059f343-4fa8-4e05-be77-28232f0efe0a.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/073/013/73013939/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/073/013/73013939/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/073/013/73013939/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 1 sequences
1[08:55:42] This is snippy 4.6.0
Show full stderr[08:55:42] This is snippy 4.6.0 [08:55:42] Written by Torsten Seemann [08:55:42] Obtained from https://github.com/tseemann/snippy [08:55:42] Detected operating system: linux [08:55:42] Enabling bundled linux tools. [08:55:42] Found bwa - /usr/local/bin/bwa [08:55:42] Found bcftools - /usr/local/bin/bcftools [08:55:42] Found samtools - /usr/local/bin/samtools [08:55:42] Found java - /usr/local/bin/java [08:55:42] Found snpEff - /usr/local/bin/snpEff [08:55:42] Found samclip - /usr/local/bin/samclip [08:55:42] Found seqtk - /usr/local/bin/seqtk [08:55:42] Found parallel - /usr/local/bin/parallel [08:55:42] Found freebayes - /usr/local/bin/freebayes [08:55:42] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:55:42] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:55:42] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:55:42] Found vcfuniq - /usr/local/bin/vcfuniq [08:55:42] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:55:42] Found gzip - /bin/gzip [08:55:42] Found vt - /usr/local/bin/vt [08:55:42] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:55:42] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:55:42] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:55:42] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:55:42] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:55:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:55:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:55:42] Using reference: /corral4/main/objects/5/2/1/dataset_52175a55-fab0-4a59-828e-1ca4a8985152.dat [08:55:42] Treating reference as 'genbank' format. [08:55:42] Will use 1 CPU cores. [08:55:42] Using read file: /corral4/main/objects/9/2/c/dataset_92c7369e-749f-48bd-8297-af9ccf3349e9.dat [08:55:42] Creating folder: PAK_resistant_Strain_zip [08:55:42] Changing working directory: PAK_resistant_Strain_zip [08:55:42] Creating reference folder: reference [08:55:42] Extracting FASTA and GFF from reference. [08:55:46] Wrote 1 sequences to ref.fa [08:55:46] Wrote 5867 features to ref.gff [08:55:46] Creating reference/snpeff.config [08:55:46] Freebayes will process 1 chunks of 6502546 bp, 1 chunks at a time. [08:55:46] Using BAM RG (Read Group) ID: PAK_resistant_Strain_zip [08:55:46] Running: samtools faidx reference/ref.fa 2>> snps.log [08:55:46] Running: bwa index reference/ref.fa 2>> snps.log [08:55:50] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [08:55:50] Running: ln -sf reference/ref.fa . 2>> snps.log [08:55:50] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [08:55:50] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [08:55:50] Running: snpEff build -c reference/snpeff.config -dataDir . -gff3 ref 2>> snps.log [08:55:57] Running: bwa mem -Y -M -R '@RG\tID:PAK_resistant_Strain_zip\tSM:PAK_resistant_Strain_zip' -t 1 reference/ref.fa /corral4/main/objects/9/2/c/dataset_92c7369e-749f-48bd-8297-af9ccf3349e9.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/073/013/73013941/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/073/013/73013941/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/073/013/73013941/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 1 sequences
1[08:55:55] This is snippy 4.6.0
Show full stderr[08:55:55] This is snippy 4.6.0 [08:55:55] Written by Torsten Seemann [08:55:55] Obtained from https://github.com/tseemann/snippy [08:55:55] Detected operating system: linux [08:55:55] Enabling bundled linux tools. [08:55:55] Found bwa - /usr/local/bin/bwa [08:55:55] Found bcftools - /usr/local/bin/bcftools [08:55:55] Found samtools - /usr/local/bin/samtools [08:55:55] Found java - /usr/local/bin/java [08:55:55] Found snpEff - /usr/local/bin/snpEff [08:55:55] Found samclip - /usr/local/bin/samclip [08:55:55] Found seqtk - /usr/local/bin/seqtk [08:55:55] Found parallel - /usr/local/bin/parallel [08:55:55] Found freebayes - /usr/local/bin/freebayes [08:55:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:55:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:55:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:55:55] Found vcfuniq - /usr/local/bin/vcfuniq [08:55:55] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:55:55] Found gzip - /bin/gzip [08:55:55] Found vt - /usr/local/bin/vt [08:55:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:55:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:55:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:55:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:55:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:55:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:55:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:55:56] Using reference: /corral4/main/objects/7/5/0/dataset_750a1866-e250-4785-864e-3176f0899da8.dat [08:55:56] Treating reference as 'genbank' format. [08:55:56] Will use 1 CPU cores. [08:55:56] Using read file: /corral4/main/objects/0/4/9/dataset_0497b5ba-1d9b-4e33-8e5d-487ce10cf95c.dat [08:55:56] Creating folder: PAK_resistant_Strain_zip [08:55:56] Changing working directory: PAK_resistant_Strain_zip [08:55:56] Creating reference folder: reference [08:55:56] Extracting FASTA and GFF from reference. [08:55:59] Wrote 1 sequences to ref.fa [08:55:59] Wrote 5867 features to ref.gff [08:55:59] Creating reference/snpeff.config [08:55:59] Freebayes will process 1 chunks of 6502546 bp, 1 chunks at a time. [08:55:59] Using BAM RG (Read Group) ID: PAK_resistant_Strain_zip [08:55:59] Running: samtools faidx reference/ref.fa 2>> snps.log [08:55:59] Running: bwa index reference/ref.fa 2>> snps.log [08:56:06] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [08:56:06] Running: ln -sf reference/ref.fa . 2>> snps.log [08:56:06] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [08:56:06] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [08:56:06] Running: snpEff build -c reference/snpeff.config -dataDir . -gff3 ref 2>> snps.log [08:56:13] Running: bwa mem -Y -M -R '@RG\tID:PAK_resistant_Strain_zip\tSM:PAK_resistant_Strain_zip' -t 1 reference/ref.fa /corral4/main/objects/0/4/9/dataset_0497b5ba-1d9b-4e33-8e5d-487ce10cf95c.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/073/013/73013943/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/073/013/73013943/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/073/013/73013943/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 1 sequences
1[08:56:04] This is snippy 4.6.0
Show full stderr[08:56:04] This is snippy 4.6.0 [08:56:04] Written by Torsten Seemann [08:56:04] Obtained from https://github.com/tseemann/snippy [08:56:04] Detected operating system: linux [08:56:04] Enabling bundled linux tools. [08:56:04] Found bwa - /usr/local/bin/bwa [08:56:04] Found bcftools - /usr/local/bin/bcftools [08:56:04] Found samtools - /usr/local/bin/samtools [08:56:04] Found java - /usr/local/bin/java [08:56:04] Found snpEff - /usr/local/bin/snpEff [08:56:04] Found samclip - /usr/local/bin/samclip [08:56:04] Found seqtk - /usr/local/bin/seqtk [08:56:05] Found parallel - /usr/local/bin/parallel [08:56:05] Found freebayes - /usr/local/bin/freebayes [08:56:05] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:56:05] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:56:05] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:56:05] Found vcfuniq - /usr/local/bin/vcfuniq [08:56:05] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:56:05] Found gzip - /bin/gzip [08:56:05] Found vt - /usr/local/bin/vt [08:56:05] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:56:05] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:56:05] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:56:05] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:56:05] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:56:06] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:56:06] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:56:06] Using reference: /corral4/main/objects/9/3/b/dataset_93b321fd-b84a-47b8-859b-82f530291683.dat [08:56:09] Treating reference as 'genbank' format. [08:56:09] Will use 1 CPU cores. [08:56:09] Using read file: /corral4/main/objects/c/0/1/dataset_c01b95e9-6e67-4f95-b75e-aae4d0b579d4.dat [08:56:09] Creating folder: PAK_resistant_Strain_zip [08:56:09] Changing working directory: PAK_resistant_Strain_zip [08:56:09] Creating reference folder: reference [08:56:09] Extracting FASTA and GFF from reference. [08:56:13] Wrote 1 sequences to ref.fa [08:56:13] Wrote 5867 features to ref.gff [08:56:13] Creating reference/snpeff.config [08:56:13] Freebayes will process 1 chunks of 6502546 bp, 1 chunks at a time. [08:56:13] Using BAM RG (Read Group) ID: PAK_resistant_Strain_zip [08:56:13] Running: samtools faidx reference/ref.fa 2>> snps.log [08:56:14] Running: bwa index reference/ref.fa 2>> snps.log [08:56:22] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [08:56:22] Running: ln -sf reference/ref.fa . 2>> snps.log [08:56:22] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [08:56:23] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [08:56:23] Running: snpEff build -c reference/snpeff.config -dataDir . -gff3 ref 2>> snps.log [08:56:31] Running: bwa mem -Y -M -R '@RG\tID:PAK_resistant_Strain_zip\tSM:PAK_resistant_Strain_zip' -t 1 reference/ref.fa /corral4/main/objects/c/0/1/dataset_c01b95e9-6e67-4f95-b75e-aae4d0b579d4.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/073/013/73013946/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/073/013/73013946/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/073/013/73013946/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 1 sequences in reference/ref.fa.fai [M::bwa_idx_load_from_di
1[08:56:31] This is snippy 4.6.0
Show full stderr[08:56:31] This is snippy 4.6.0 [08:56:31] Written by Torsten Seemann [08:56:31] Obtained from https://github.com/tseemann/snippy [08:56:31] Detected operating system: linux [08:56:31] Enabling bundled linux tools. [08:56:31] Found bwa - /usr/local/bin/bwa [08:56:31] Found bcftools - /usr/local/bin/bcftools [08:56:31] Found samtools - /usr/local/bin/samtools [08:56:31] Found java - /usr/local/bin/java [08:56:31] Found snpEff - /usr/local/bin/snpEff [08:56:31] Found samclip - /usr/local/bin/samclip [08:56:31] Found seqtk - /usr/local/bin/seqtk [08:56:31] Found parallel - /usr/local/bin/parallel [08:56:31] Found freebayes - /usr/local/bin/freebayes [08:56:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:56:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:56:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:56:31] Found vcfuniq - /usr/local/bin/vcfuniq [08:56:31] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:56:31] Found gzip - /bin/gzip [08:56:31] Found vt - /usr/local/bin/vt [08:56:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:56:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:56:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:56:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:56:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:56:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:56:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:56:31] Using reference: /corral4/main/objects/c/c/c/dataset_ccc76921-13cc-409b-ab75-a966e36a5169.dat [08:56:32] Treating reference as 'genbank' format. [08:56:32] Will use 1 CPU cores. [08:56:32] Using read file: /corral4/main/objects/a/e/0/dataset_ae0fae57-731f-4dbf-9965-c646cbb4af08.dat [08:56:32] Creating folder: PAK_resistant_Strain_zip [08:56:32] Changing working directory: PAK_resistant_Strain_zip [08:56:32] Creating reference folder: reference [08:56:32] Extracting FASTA and GFF from reference. [08:56:35] Wrote 1 sequences to ref.fa [08:56:35] Wrote 5867 features to ref.gff [08:56:35] Creating reference/snpeff.config [08:56:35] Freebayes will process 1 chunks of 6502546 bp, 1 chunks at a time. [08:56:35] Using BAM RG (Read Group) ID: PAK_resistant_Strain_zip [08:56:35] Running: samtools faidx reference/ref.fa 2>> snps.log [08:56:35] Running: bwa index reference/ref.fa 2>> snps.log [08:56:39] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [08:56:39] Running: ln -sf reference/ref.fa . 2>> snps.log [08:56:39] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [08:56:39] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [08:56:39] Running: snpEff build -c reference/snpeff.config -dataDir . -gff3 ref 2>> snps.log [08:56:45] Running: bwa mem -Y -M -R '@RG\tID:PAK_resistant_Strain_zip\tSM:PAK_resistant_Strain_zip' -t 1 reference/ref.fa /corral4/main/objects/a/e/0/dataset_ae0fae57-731f-4dbf-9965-c646cbb4af08.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/073/013/73013955/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/073/013/73013955/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/073/013/73013955/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 1 sequences
1[08:56:40] This is snippy 4.6.0
Show full stderr[08:56:40] This is snippy 4.6.0 [08:56:40] Written by Torsten Seemann [08:56:40] Obtained from https://github.com/tseemann/snippy [08:56:40] Detected operating system: linux [08:56:40] Enabling bundled linux tools. [08:56:40] Found bwa - /usr/local/bin/bwa [08:56:40] Found bcftools - /usr/local/bin/bcftools [08:56:40] Found samtools - /usr/local/bin/samtools [08:56:40] Found java - /usr/local/bin/java [08:56:40] Found snpEff - /usr/local/bin/snpEff [08:56:40] Found samclip - /usr/local/bin/samclip [08:56:40] Found seqtk - /usr/local/bin/seqtk [08:56:40] Found parallel - /usr/local/bin/parallel [08:56:40] Found freebayes - /usr/local/bin/freebayes [08:56:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:56:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:56:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:56:40] Found vcfuniq - /usr/local/bin/vcfuniq [08:56:40] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:56:40] Found gzip - /bin/gzip [08:56:40] Found vt - /usr/local/bin/vt [08:56:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:56:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:56:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:56:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:56:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:56:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:56:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:56:40] Using reference: /corral4/main/objects/8/9/f/dataset_89f708b0-3a33-4393-bb58-3e663bcb13fe.dat [08:56:41] Treating reference as 'genbank' format. [08:56:41] Will use 1 CPU cores. [08:56:41] Using read file: /corral4/main/objects/4/0/e/dataset_40e578c2-e503-4958-95f2-763b8d2f4796.dat [08:56:41] Creating folder: PAK_resistant_Strain_zip [08:56:41] Changing working directory: PAK_resistant_Strain_zip [08:56:41] Creating reference folder: reference [08:56:41] Extracting FASTA and GFF from reference. [08:56:44] Wrote 1 sequences to ref.fa [08:56:44] Wrote 5867 features to ref.gff [08:56:44] Creating reference/snpeff.config [08:56:44] Freebayes will process 1 chunks of 6502546 bp, 1 chunks at a time. [08:56:44] Using BAM RG (Read Group) ID: PAK_resistant_Strain_zip [08:56:44] Running: samtools faidx reference/ref.fa 2>> snps.log [08:56:44] Running: bwa index reference/ref.fa 2>> snps.log [08:56:48] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [08:56:48] Running: ln -sf reference/ref.fa . 2>> snps.log [08:56:48] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [08:56:48] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [08:56:48] Running: snpEff build -c reference/snpeff.config -dataDir . -gff3 ref 2>> snps.log [08:56:54] Running: bwa mem -Y -M -R '@RG\tID:PAK_resistant_Strain_zip\tSM:PAK_resistant_Strain_zip' -t 1 reference/ref.fa /corral4/main/objects/4/0/e/dataset_40e578c2-e503-4958-95f2-763b8d2f4796.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/073/013/73013963/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/073/013/73013963/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/073/013/73013963/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 1 sequences
1[08:57:55] This is snippy 4.6.0
Show full stderr[08:57:55] This is snippy 4.6.0 [08:57:55] Written by Torsten Seemann [08:57:55] Obtained from https://github.com/tseemann/snippy [08:57:55] Detected operating system: linux [08:57:55] Enabling bundled linux tools. [08:57:55] Found bwa - /usr/local/bin/bwa [08:57:55] Found bcftools - /usr/local/bin/bcftools [08:57:55] Found samtools - /usr/local/bin/samtools [08:57:55] Found java - /usr/local/bin/java [08:57:55] Found snpEff - /usr/local/bin/snpEff [08:57:55] Found samclip - /usr/local/bin/samclip [08:57:55] Found seqtk - /usr/local/bin/seqtk [08:57:55] Found parallel - /usr/local/bin/parallel [08:57:55] Found freebayes - /usr/local/bin/freebayes [08:57:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [08:57:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [08:57:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [08:57:55] Found vcfuniq - /usr/local/bin/vcfuniq [08:57:55] Found vcffirstheader - /usr/local/bin/vcffirstheader [08:57:55] Found gzip - /bin/gzip [08:57:55] Found vt - /usr/local/bin/vt [08:57:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [08:57:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [08:57:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [08:57:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [08:57:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [08:57:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [08:57:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [08:57:56] Using reference: /corral4/main/objects/6/7/d/dataset_67dc2d8d-ac2c-40ad-98bd-47ceff4d01ae.dat [08:57:56] Treating reference as 'genbank' format. [08:57:56] Will use 1 CPU cores. [08:57:56] Using read file: /corral4/main/objects/d/8/e/dataset_d8ebdec0-6eff-408f-be70-4806857fadcf.dat [08:57:56] Creating folder: PAK_resistant_Strain_zip [08:57:56] Changing working directory: PAK_resistant_Strain_zip [08:57:56] Creating reference folder: reference [08:57:56] Extracting FASTA and GFF from reference. [08:57:59] Wrote 1 sequences to ref.fa [08:57:59] Wrote 5867 features to ref.gff [08:57:59] Creating reference/snpeff.config [08:57:59] Freebayes will process 1 chunks of 6502546 bp, 1 chunks at a time. [08:57:59] Using BAM RG (Read Group) ID: PAK_resistant_Strain_zip [08:57:59] Running: samtools faidx reference/ref.fa 2>> snps.log [08:57:59] Running: bwa index reference/ref.fa 2>> snps.log [08:58:05] Error running command, check PAK_resistant_Strain_zip/snps.log
1[09:02:03] This is snippy 4.6.0
Show full stderr[09:02:03] This is snippy 4.6.0 [09:02:03] Written by Torsten Seemann [09:02:03] Obtained from https://github.com/tseemann/snippy [09:02:03] Detected operating system: linux [09:02:03] Enabling bundled linux tools. [09:02:03] Found bwa - /usr/local/bin/bwa [09:02:03] Found bcftools - /usr/local/bin/bcftools [09:02:03] Found samtools - /usr/local/bin/samtools [09:02:03] Found java - /usr/local/bin/java [09:02:03] Found snpEff - /usr/local/bin/snpEff [09:02:03] Found samclip - /usr/local/bin/samclip [09:02:03] Found seqtk - /usr/local/bin/seqtk [09:02:03] Found parallel - /usr/local/bin/parallel [09:02:03] Found freebayes - /usr/local/bin/freebayes [09:02:03] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [09:02:03] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [09:02:03] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [09:02:03] Found vcfuniq - /usr/local/bin/vcfuniq [09:02:03] Found vcffirstheader - /usr/local/bin/vcffirstheader [09:02:03] Found gzip - /bin/gzip [09:02:03] Found vt - /usr/local/bin/vt [09:02:03] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [09:02:03] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [09:02:03] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [09:02:03] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [09:02:03] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [09:02:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [09:02:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [09:02:04] Using reference: /corral4/main/objects/8/9/f/dataset_89f708b0-3a33-4393-bb58-3e663bcb13fe.dat [09:02:04] Treating reference as 'genbank' format. [09:02:04] Will use 1 CPU cores. [09:02:04] Using read file: /corral4/main/objects/4/0/e/dataset_40e578c2-e503-4958-95f2-763b8d2f4796.dat [09:02:04] Creating folder: PAK_resistant_Strain_zip [09:02:04] Changing working directory: PAK_resistant_Strain_zip [09:02:04] Creating reference folder: reference [09:02:04] Extracting FASTA and GFF from reference. [09:02:08] Wrote 1 sequences to ref.fa [09:02:08] Wrote 5867 features to ref.gff [09:02:08] Creating reference/snpeff.config [09:02:08] Freebayes will process 1 chunks of 6502546 bp, 1 chunks at a time. [09:02:08] Using BAM RG (Read Group) ID: PAK_resistant_Strain_zip [09:02:08] Running: samtools faidx reference/ref.fa 2>> snps.log [09:02:08] Running: bwa index reference/ref.fa 2>> snps.log [09:02:15] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [09:02:15] Running: ln -sf reference/ref.fa . 2>> snps.log [09:02:15] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [09:02:16] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [09:02:16] Running: snpEff build -c reference/snpeff.config -dataDir . -gff3 ref 2>> snps.log [09:02:23] Running: bwa mem -Y -M -R '@RG\tID:PAK_resistant_Strain_zip\tSM:PAK_resistant_Strain_zip' -t 1 reference/ref.fa /corral4/main/objects/4/0/e/dataset_40e578c2-e503-4958-95f2-763b8d2f4796.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/073/014/73014267/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/073/014/73014267/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/073/014/73014267/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 1 sequences
1[09:02:31] This is snippy 4.6.0
Show full stderr[09:02:31] This is snippy 4.6.0 [09:02:31] Written by Torsten Seemann [09:02:31] Obtained from https://github.com/tseemann/snippy [09:02:31] Detected operating system: linux [09:02:31] Enabling bundled linux tools. [09:02:31] Found bwa - /usr/local/bin/bwa [09:02:31] Found bcftools - /usr/local/bin/bcftools [09:02:31] Found samtools - /usr/local/bin/samtools [09:02:31] Found java - /usr/local/bin/java [09:02:31] Found snpEff - /usr/local/bin/snpEff [09:02:31] Found samclip - /usr/local/bin/samclip [09:02:31] Found seqtk - /usr/local/bin/seqtk [09:02:31] Found parallel - /usr/local/bin/parallel [09:02:31] Found freebayes - /usr/local/bin/freebayes [09:02:31] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [09:02:31] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [09:02:31] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [09:02:31] Found vcfuniq - /usr/local/bin/vcfuniq [09:02:31] Found vcffirstheader - /usr/local/bin/vcffirstheader [09:02:31] Found gzip - /bin/gzip [09:02:31] Found vt - /usr/local/bin/vt [09:02:31] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [09:02:31] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [09:02:31] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [09:02:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [09:02:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [09:02:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [09:02:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [09:02:32] Using reference: /corral4/main/objects/2/8/b/dataset_28bc974e-ae27-4c84-ba56-8144b48f519d.dat [09:02:32] Treating reference as 'fasta' format. [09:02:32] Will use 1 CPU cores. [09:02:32] Using read file: /corral4/main/objects/0/4/9/dataset_0497b5ba-1d9b-4e33-8e5d-487ce10cf95c.dat [09:02:32] Creating folder: PAK_resistant_Strain_zip [09:02:32] Changing working directory: PAK_resistant_Strain_zip [09:02:32] Creating reference folder: reference [09:02:32] Extracting FASTA and GFF from reference. [09:02:32] Wrote 1 sequences to ref.fa [09:02:32] Wrote 0 features to ref.gff [09:02:32] Freebayes will process 1 chunks of 6502547 bp, 1 chunks at a time. [09:02:32] Using BAM RG (Read Group) ID: PAK_resistant_Strain_zip [09:02:32] Running: samtools faidx reference/ref.fa 2>> snps.log [09:02:32] Running: bwa index reference/ref.fa 2>> snps.log [09:02:37] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [09:02:37] Running: ln -sf reference/ref.fa . 2>> snps.log [09:02:37] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [09:02:37] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [09:02:37] Running: bwa mem -Y -M -R '@RG\tID:PAK_resistant_Strain_zip\tSM:PAK_resistant_Strain_zip' -t 1 reference/ref.fa /corral4/main/objects/0/4/9/dataset_0497b5ba-1d9b-4e33-8e5d-487ce10cf95c.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/073/014/73014271/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/073/014/73014271/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/073/014/73014271/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 1 sequences in reference/ref.fa.fai [M::process] read 67296 sequences (10000219 bp)... [M::process] read 67246 sequences (10000197 bp)... [M::mem_process_s
1[09:20:35] This is snippy 4.6.0
Show full stderr[09:20:35] This is snippy 4.6.0 [09:20:35] Written by Torsten Seemann [09:20:35] Obtained from https://github.com/tseemann/snippy [09:20:35] Detected operating system: linux [09:20:35] Enabling bundled linux tools. [09:20:35] Found bwa - /usr/local/bin/bwa [09:20:35] Found bcftools - /usr/local/bin/bcftools [09:20:35] Found samtools - /usr/local/bin/samtools [09:20:35] Found java - /usr/local/bin/java [09:20:35] Found snpEff - /usr/local/bin/snpEff [09:20:35] Found samclip - /usr/local/bin/samclip [09:20:35] Found seqtk - /usr/local/bin/seqtk [09:20:35] Found parallel - /usr/local/bin/parallel [09:20:35] Found freebayes - /usr/local/bin/freebayes [09:20:36] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [09:20:36] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [09:20:36] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [09:20:36] Found vcfuniq - /usr/local/bin/vcfuniq [09:20:36] Found vcffirstheader - /usr/local/bin/vcffirstheader [09:20:36] Found gzip - /bin/gzip [09:20:36] Found vt - /usr/local/bin/vt [09:20:36] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [09:20:36] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [09:20:36] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [09:20:36] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [09:20:36] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [09:20:37] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [09:20:37] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [09:20:37] Using reference: /corral4/main/objects/3/6/9/dataset_3695ece0-8574-430e-be45-4d83063106f4.dat [09:20:37] Treating reference as 'genbank' format. [09:20:37] Will use 1 CPU cores. [09:20:37] Using read file: /corral4/main/objects/c/2/9/dataset_c29f6af4-20e0-4ae3-bf5e-b07e4f6be1b4.dat [09:20:37] Creating folder: KPC_42_trim_fastq [09:20:37] Changing working directory: KPC_42_trim_fastq [09:20:37] Creating reference folder: reference [09:20:37] Extracting FASTA and GFF from reference. [09:20:41] Wrote 4 sequences to ref.fa [09:20:41] Wrote 5625 features to ref.gff [09:20:41] Creating reference/snpeff.config [09:20:41] Freebayes will process 1 chunks of 5745542 bp, 1 chunks at a time. [09:20:41] Using BAM RG (Read Group) ID: KPC_42_trim_fastq [09:20:41] Running: samtools faidx reference/ref.fa 2>> snps.log [09:20:41] Running: bwa index reference/ref.fa 2>> snps.log [09:20:44] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [09:20:44] Running: ln -sf reference/ref.fa . 2>> snps.log [09:20:44] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [09:20:44] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [09:20:45] Running: snpEff build -c reference/snpeff.config -dataDir . -gff3 ref 2>> snps.log [09:20:49] Error running command, check KPC_42_trim_fastq/snps.log
1tar: pECC231/snps.bam: Cannot close: Disk quota exceeded
Show full stderrtar: pECC231/snps.bam: Cannot close: Disk quota exceeded tar: Exiting with failure status due to previous errors
1[15:58:00] This is snippy 4.6.0
Show full stderr[15:58:00] This is snippy 4.6.0 [15:58:00] Written by Torsten Seemann [15:58:00] Obtained from https://github.com/tseemann/snippy [15:58:00] Detected operating system: linux [15:58:00] Enabling bundled linux tools. [15:58:00] Found bwa - /usr/local/bin/bwa [15:58:00] Found bcftools - /usr/local/bin/bcftools [15:58:00] Found samtools - /usr/local/bin/samtools [15:58:00] Found java - /usr/local/bin/java [15:58:00] Found snpEff - /usr/local/bin/snpEff [15:58:00] Found samclip - /usr/local/bin/samclip [15:58:00] Found seqtk - /usr/local/bin/seqtk [15:58:00] Found parallel - /usr/local/bin/parallel [15:58:00] Found freebayes - /usr/local/bin/freebayes [15:58:00] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [15:58:00] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [15:58:00] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [15:58:00] Found vcfuniq - /usr/local/bin/vcfuniq [15:58:00] Found vcffirstheader - /usr/local/bin/vcffirstheader [15:58:00] Found gzip - /bin/gzip [15:58:00] Found vt - /usr/local/bin/vt [15:58:00] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [15:58:00] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [15:58:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [15:58:01] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [15:58:01] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [15:58:03] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [15:58:03] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [15:58:03] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:56:54] This is snippy 4.6.0
Show full stderr[14:56:54] This is snippy 4.6.0 [14:56:54] Written by Torsten Seemann [14:56:54] Obtained from https://github.com/tseemann/snippy [14:56:54] Detected operating system: linux [14:56:54] Enabling bundled linux tools. [14:56:54] Found bwa - /usr/local/bin/bwa [14:56:54] Found bcftools - /usr/local/bin/bcftools [14:56:54] Found samtools - /usr/local/bin/samtools [14:56:54] Found java - /usr/local/bin/java [14:56:54] Found snpEff - /usr/local/bin/snpEff [14:56:54] Found samclip - /usr/local/bin/samclip [14:56:54] Found seqtk - /usr/local/bin/seqtk [14:56:54] Found parallel - /usr/local/bin/parallel [14:56:54] Found freebayes - /usr/local/bin/freebayes [14:56:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:56:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:56:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:56:54] Found vcfuniq - /usr/local/bin/vcfuniq [14:56:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:56:54] Found gzip - /bin/gzip [14:56:54] Found vt - /usr/local/bin/vt [14:56:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:56:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:56:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:56:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:56:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:56:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:56:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:56:55] Using reference: /corral4/main/objects/a/5/1/dataset_a5160a31-fbb6-42eb-8aa5-a52875760c5c.dat [14:56:55] Could not guess format '/corral4/main/objects/a/5/1/dataset_a5160a31-fbb6-42eb-8aa5-a52875760c5c.dat'
1[17:04:32] This is snippy 4.6.0
Show full stderr[17:04:32] This is snippy 4.6.0 [17:04:32] Written by Torsten Seemann [17:04:32] Obtained from https://github.com/tseemann/snippy [17:04:32] Detected operating system: linux [17:04:32] Enabling bundled linux tools. [17:04:32] Found bwa - /usr/local/bin/bwa [17:04:32] Found bcftools - /usr/local/bin/bcftools [17:04:32] Found samtools - /usr/local/bin/samtools [17:04:32] Found java - /usr/local/bin/java [17:04:32] Found snpEff - /usr/local/bin/snpEff [17:04:32] Found samclip - /usr/local/bin/samclip [17:04:32] Found seqtk - /usr/local/bin/seqtk [17:04:32] Found parallel - /usr/local/bin/parallel [17:04:32] Found freebayes - /usr/local/bin/freebayes [17:04:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [17:04:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [17:04:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [17:04:32] Found vcfuniq - /usr/local/bin/vcfuniq [17:04:32] Found vcffirstheader - /usr/local/bin/vcffirstheader [17:04:32] Found gzip - /bin/gzip [17:04:32] Found vt - /usr/local/bin/vt [17:04:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [17:04:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [17:04:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [17:04:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [17:04:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [17:04:32] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [17:04:32] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [17:04:32] Using reference: /jetstream2/scratch/main/jobs/73095304/inputs/dataset_a5160a31-fbb6-42eb-8aa5-a52875760c5c.dat [17:04:32] Could not guess format '/jetstream2/scratch/main/jobs/73095304/inputs/dataset_a5160a31-fbb6-42eb-8aa5-a52875760c5c.dat'
1[23:42:45] This is snippy 4.6.0
Show full stderr[23:42:45] This is snippy 4.6.0 [23:42:45] Written by Torsten Seemann [23:42:45] Obtained from https://github.com/tseemann/snippy [23:42:45] Detected operating system: linux [23:42:45] Enabling bundled linux tools. [23:42:45] Found bwa - /usr/local/bin/bwa [23:42:45] Found bcftools - /usr/local/bin/bcftools [23:42:45] Found samtools - /usr/local/bin/samtools [23:42:45] Found java - /usr/local/bin/java [23:42:45] Found snpEff - /usr/local/bin/snpEff [23:42:45] Found samclip - /usr/local/bin/samclip [23:42:45] Found seqtk - /usr/local/bin/seqtk [23:42:45] Found parallel - /usr/local/bin/parallel [23:42:45] Found freebayes - /usr/local/bin/freebayes [23:42:45] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [23:42:45] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [23:42:45] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [23:42:45] Found vcfuniq - /usr/local/bin/vcfuniq [23:42:45] Found vcffirstheader - /usr/local/bin/vcffirstheader [23:42:45] Found gzip - /bin/gzip [23:42:45] Found vt - /usr/local/bin/vt [23:42:45] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [23:42:45] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [23:42:45] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [23:42:46] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [23:42:46] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [23:42:46] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [23:42:46] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [23:42:46] Please supply a reference FASTA/GBK/EMBL file with --reference
1[23:45:57] This is snippy 4.6.0
Show full stderr[23:45:57] This is snippy 4.6.0 [23:45:57] Written by Torsten Seemann [23:45:57] Obtained from https://github.com/tseemann/snippy [23:45:57] Detected operating system: linux [23:45:57] Enabling bundled linux tools. [23:45:57] Found bwa - /usr/local/bin/bwa [23:45:57] Found bcftools - /usr/local/bin/bcftools [23:45:57] Found samtools - /usr/local/bin/samtools [23:45:57] Found java - /usr/local/bin/java [23:45:57] Found snpEff - /usr/local/bin/snpEff [23:45:57] Found samclip - /usr/local/bin/samclip [23:45:57] Found seqtk - /usr/local/bin/seqtk [23:45:57] Found parallel - /usr/local/bin/parallel [23:45:57] Found freebayes - /usr/local/bin/freebayes [23:45:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [23:45:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [23:45:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [23:45:57] Found vcfuniq - /usr/local/bin/vcfuniq [23:45:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [23:45:57] Found gzip - /bin/gzip [23:45:57] Found vt - /usr/local/bin/vt [23:45:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [23:45:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [23:45:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [23:45:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [23:45:58] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [23:45:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [23:45:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [23:45:58] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:02:28] This is snippy 4.6.0
Show full stderr[00:02:28] This is snippy 4.6.0 [00:02:28] Written by Torsten Seemann [00:02:28] Obtained from https://github.com/tseemann/snippy [00:02:28] Detected operating system: linux [00:02:28] Enabling bundled linux tools. [00:02:28] Found bwa - /usr/local/bin/bwa [00:02:28] Found bcftools - /usr/local/bin/bcftools [00:02:28] Found samtools - /usr/local/bin/samtools [00:02:28] Found java - /usr/local/bin/java [00:02:28] Found snpEff - /usr/local/bin/snpEff [00:02:28] Found samclip - /usr/local/bin/samclip [00:02:28] Found seqtk - /usr/local/bin/seqtk [00:02:29] Found parallel - /usr/local/bin/parallel [00:02:29] Found freebayes - /usr/local/bin/freebayes [00:02:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:02:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:02:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:02:29] Found vcfuniq - /usr/local/bin/vcfuniq [00:02:29] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:02:29] Found gzip - /bin/gzip [00:02:29] Found vt - /usr/local/bin/vt [00:02:29] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:02:29] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:02:29] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:02:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:02:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:02:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:02:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:02:29] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:11:40] This is snippy 4.6.0
Show full stderr[07:11:40] This is snippy 4.6.0 [07:11:40] Written by Torsten Seemann [07:11:40] Obtained from https://github.com/tseemann/snippy [07:11:40] Detected operating system: linux [07:11:40] Enabling bundled linux tools. [07:11:40] Found bwa - /usr/local/bin/bwa [07:11:40] Found bcftools - /usr/local/bin/bcftools [07:11:40] Found samtools - /usr/local/bin/samtools [07:11:40] Found java - /usr/local/bin/java [07:11:40] Found snpEff - /usr/local/bin/snpEff [07:11:40] Found samclip - /usr/local/bin/samclip [07:11:40] Found seqtk - /usr/local/bin/seqtk [07:11:40] Found parallel - /usr/local/bin/parallel [07:11:40] Found freebayes - /usr/local/bin/freebayes [07:11:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:11:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:11:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:11:40] Found vcfuniq - /usr/local/bin/vcfuniq [07:11:40] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:11:40] Found gzip - /bin/gzip [07:11:40] Found vt - /usr/local/bin/vt [07:11:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:11:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:11:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:11:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:11:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:11:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:11:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:11:42] Using reference: /corral4/main/objects/b/3/5/dataset_b355f287-7d9e-49b8-b0db-adb9b89cf8a2.dat [07:11:42] Could not guess format '/corral4/main/objects/b/3/5/dataset_b355f287-7d9e-49b8-b0db-adb9b89cf8a2.dat'
1[09:17:53] This is snippy 4.6.0
Show full stderr[09:17:53] This is snippy 4.6.0 [09:17:53] Written by Torsten Seemann [09:17:53] Obtained from https://github.com/tseemann/snippy [09:17:53] Detected operating system: linux [09:17:53] Enabling bundled linux tools. [09:17:53] Found bwa - /usr/local/bin/bwa [09:17:53] Found bcftools - /usr/local/bin/bcftools [09:17:53] Found samtools - /usr/local/bin/samtools [09:17:53] Found java - /usr/local/bin/java [09:17:53] Found snpEff - /usr/local/bin/snpEff [09:17:53] Found samclip - /usr/local/bin/samclip [09:17:53] Found seqtk - /usr/local/bin/seqtk [09:17:53] Found parallel - /usr/local/bin/parallel [09:17:54] Found freebayes - /usr/local/bin/freebayes [09:17:54] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [09:17:54] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [09:17:54] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [09:17:54] Found vcfuniq - /usr/local/bin/vcfuniq [09:17:54] Found vcffirstheader - /usr/local/bin/vcffirstheader [09:17:54] Found gzip - /bin/gzip [09:17:54] Found vt - /usr/local/bin/vt [09:17:54] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [09:17:54] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [09:17:54] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [09:17:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [09:17:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [09:17:55] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [09:17:55] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [09:17:55] Please supply a reference FASTA/GBK/EMBL file with --reference
1[09:21:11] This is snippy 4.6.0
Show full stderr[09:21:11] This is snippy 4.6.0 [09:21:11] Written by Torsten Seemann [09:21:11] Obtained from https://github.com/tseemann/snippy [09:21:11] Detected operating system: linux [09:21:11] Enabling bundled linux tools. [09:21:11] Found bwa - /usr/local/bin/bwa [09:21:11] Found bcftools - /usr/local/bin/bcftools [09:21:11] Found samtools - /usr/local/bin/samtools [09:21:11] Found java - /usr/local/bin/java [09:21:11] Found snpEff - /usr/local/bin/snpEff [09:21:11] Found samclip - /usr/local/bin/samclip [09:21:11] Found seqtk - /usr/local/bin/seqtk [09:21:11] Found parallel - /usr/local/bin/parallel [09:21:11] Found freebayes - /usr/local/bin/freebayes [09:21:11] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [09:21:11] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [09:21:11] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [09:21:11] Found vcfuniq - /usr/local/bin/vcfuniq [09:21:11] Found vcffirstheader - /usr/local/bin/vcffirstheader [09:21:11] Found gzip - /bin/gzip [09:21:11] Found vt - /usr/local/bin/vt [09:21:11] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [09:21:11] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [09:21:11] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [09:21:11] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [09:21:11] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [09:21:12] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [09:21:12] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [09:21:12] Please supply a reference FASTA/GBK/EMBL file with --reference
1[10:47:05] This is snippy 4.6.0
Show full stderr[10:47:05] This is snippy 4.6.0 [10:47:05] Written by Torsten Seemann [10:47:05] Obtained from https://github.com/tseemann/snippy [10:47:05] Detected operating system: linux [10:47:05] Enabling bundled linux tools. [10:47:05] Found bwa - /usr/local/bin/bwa [10:47:05] Found bcftools - /usr/local/bin/bcftools [10:47:05] Found samtools - /usr/local/bin/samtools [10:47:05] Found java - /usr/local/bin/java [10:47:05] Found snpEff - /usr/local/bin/snpEff [10:47:05] Found samclip - /usr/local/bin/samclip [10:47:05] Found seqtk - /usr/local/bin/seqtk [10:47:05] Found parallel - /usr/local/bin/parallel [10:47:06] Found freebayes - /usr/local/bin/freebayes [10:47:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [10:47:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [10:47:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [10:47:06] Found vcfuniq - /usr/local/bin/vcfuniq [10:47:06] Found vcffirstheader - /usr/local/bin/vcffirstheader [10:47:06] Found gzip - /bin/gzip [10:47:06] Found vt - /usr/local/bin/vt [10:47:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [10:47:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [10:47:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [10:47:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [10:47:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [10:47:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [10:47:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [10:47:07] Using reference: /corral4/main/objects/7/8/c/dataset_78c04d78-cbdd-48cc-aaf1-b4db1ac78784.dat [10:47:07] Treating reference as 'genbank' format. [10:47:07] Will use 1 CPU cores. [10:47:07] Using read file: /corral4/main/objects/7/7/b/dataset_77b100f5-7e0e-469f-8f2b-80d4094518a1.dat [10:47:07] Creating folder: SRR36266170_fastq_gz [10:47:07] Changing working directory: SRR36266170_fastq_gz [10:47:07] Creating reference folder: reference [10:47:07] Extracting FASTA and GFF from reference. [10:47:10] Wrote 1 sequences to ref.fa [10:47:10] Wrote 4111 features to ref.gff [10:47:10] Creating reference/snpeff.config [10:47:10] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time. [10:47:10] Using BAM RG (Read Group) ID: SRR36266170_fastq_gz [10:47:10] Running: samtools faidx reference/ref.fa 2>> snps.log [10:47:10] Error running command, check SRR36266170_fastq_gz/snps.log
1[10:54:14] This is snippy 4.6.0
Show full stderr[10:54:14] This is snippy 4.6.0 [10:54:14] Written by Torsten Seemann [10:54:14] Obtained from https://github.com/tseemann/snippy [10:54:14] Detected operating system: linux [10:54:14] Enabling bundled linux tools. [10:54:14] Found bwa - /usr/local/bin/bwa [10:54:14] Found bcftools - /usr/local/bin/bcftools [10:54:14] Found samtools - /usr/local/bin/samtools [10:54:14] Found java - /usr/local/bin/java [10:54:14] Found snpEff - /usr/local/bin/snpEff [10:54:14] Found samclip - /usr/local/bin/samclip [10:54:14] Found seqtk - /usr/local/bin/seqtk [10:54:14] Found parallel - /usr/local/bin/parallel [10:54:14] Found freebayes - /usr/local/bin/freebayes [10:54:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [10:54:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [10:54:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [10:54:14] Found vcfuniq - /usr/local/bin/vcfuniq [10:54:14] Found vcffirstheader - /usr/local/bin/vcffirstheader [10:54:14] Found gzip - /bin/gzip [10:54:14] Found vt - /usr/local/bin/vt [10:54:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [10:54:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [10:54:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [10:54:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [10:54:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [10:54:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [10:54:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [10:54:15] Using reference: /corral4/main/objects/b/0/5/dataset_b05b06e7-abfd-45a9-92bf-d943a6cb035c.dat [10:54:15] Could not guess format '/corral4/main/objects/b/0/5/dataset_b05b06e7-abfd-45a9-92bf-d943a6cb035c.dat'
1[10:58:32] This is snippy 4.6.0
Show full stderr[10:58:32] This is snippy 4.6.0 [10:58:32] Written by Torsten Seemann [10:58:32] Obtained from https://github.com/tseemann/snippy [10:58:32] Detected operating system: linux [10:58:32] Enabling bundled linux tools. [10:58:32] Found bwa - /usr/local/bin/bwa [10:58:32] Found bcftools - /usr/local/bin/bcftools [10:58:32] Found samtools - /usr/local/bin/samtools [10:58:32] Found java - /usr/local/bin/java [10:58:32] Found snpEff - /usr/local/bin/snpEff [10:58:32] Found samclip - /usr/local/bin/samclip [10:58:32] Found seqtk - /usr/local/bin/seqtk [10:58:32] Found parallel - /usr/local/bin/parallel [10:58:32] Found freebayes - /usr/local/bin/freebayes [10:58:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [10:58:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [10:58:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [10:58:32] Found vcfuniq - /usr/local/bin/vcfuniq [10:58:32] Found vcffirstheader - /usr/local/bin/vcffirstheader [10:58:32] Found gzip - /bin/gzip [10:58:32] Found vt - /usr/local/bin/vt [10:58:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [10:58:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [10:58:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [10:58:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [10:58:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [10:58:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [10:58:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [10:58:33] Using reference: /corral4/main/objects/b/0/5/dataset_b05b06e7-abfd-45a9-92bf-d943a6cb035c.dat [10:58:33] Could not guess format '/corral4/main/objects/b/0/5/dataset_b05b06e7-abfd-45a9-92bf-d943a6cb035c.dat'
1[22:28:23] This is snippy 4.6.0
Show full stderr[22:28:23] This is snippy 4.6.0 [22:28:23] Written by Torsten Seemann [22:28:23] Obtained from https://github.com/tseemann/snippy [22:28:23] Detected operating system: linux [22:28:23] Enabling bundled linux tools. [22:28:23] Found bwa - /usr/local/bin/bwa [22:28:23] Found bcftools - /usr/local/bin/bcftools [22:28:23] Found samtools - /usr/local/bin/samtools [22:28:23] Found java - /usr/local/bin/java [22:28:23] Found snpEff - /usr/local/bin/snpEff [22:28:23] Found samclip - /usr/local/bin/samclip [22:28:23] Found seqtk - /usr/local/bin/seqtk [22:28:23] Found parallel - /usr/local/bin/parallel [22:28:23] Found freebayes - /usr/local/bin/freebayes [22:28:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [22:28:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [22:28:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [22:28:23] Found vcfuniq - /usr/local/bin/vcfuniq [22:28:23] Found vcffirstheader - /usr/local/bin/vcffirstheader [22:28:23] Found gzip - /bin/gzip [22:28:23] Found vt - /usr/local/bin/vt [22:28:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [22:28:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [22:28:23] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [22:28:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [22:28:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [22:28:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [22:28:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [22:28:24] Please supply a reference FASTA/GBK/EMBL file with --reference
1[12:27:57] This is snippy 4.6.0
Show full stderr[12:27:57] This is snippy 4.6.0 [12:27:57] Written by Torsten Seemann [12:27:57] Obtained from https://github.com/tseemann/snippy [12:27:57] Detected operating system: linux [12:27:57] Enabling bundled linux tools. [12:27:57] Found bwa - /usr/local/bin/bwa [12:27:57] Found bcftools - /usr/local/bin/bcftools [12:27:57] Found samtools - /usr/local/bin/samtools [12:27:57] Found java - /usr/local/bin/java [12:27:57] Found snpEff - /usr/local/bin/snpEff [12:27:57] Found samclip - /usr/local/bin/samclip [12:27:57] Found seqtk - /usr/local/bin/seqtk [12:27:57] Found parallel - /usr/local/bin/parallel [12:27:57] Found freebayes - /usr/local/bin/freebayes [12:27:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [12:27:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [12:27:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:27:57] Found vcfuniq - /usr/local/bin/vcfuniq [12:27:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:27:57] Found gzip - /bin/gzip [12:27:57] Found vt - /usr/local/bin/vt [12:27:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [12:27:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [12:27:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [12:27:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [12:27:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [12:27:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [12:27:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:27:58] Please supply a reference FASTA/GBK/EMBL file with --reference
1[21:23:53] This is snippy 4.6.0
Show full stderr[21:23:53] This is snippy 4.6.0 [21:23:53] Written by Torsten Seemann [21:23:53] Obtained from https://github.com/tseemann/snippy [21:23:53] Detected operating system: linux [21:23:53] Enabling bundled linux tools. [21:23:53] Found bwa - /usr/local/bin/bwa [21:23:53] Found bcftools - /usr/local/bin/bcftools [21:23:53] Found samtools - /usr/local/bin/samtools [21:23:53] Found java - /usr/local/bin/java [21:23:53] Found snpEff - /usr/local/bin/snpEff [21:23:53] Found samclip - /usr/local/bin/samclip [21:23:53] Found seqtk - /usr/local/bin/seqtk [21:23:53] Found parallel - /usr/local/bin/parallel [21:23:53] Found freebayes - /usr/local/bin/freebayes [21:23:53] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:23:53] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:23:53] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:23:53] Found vcfuniq - /usr/local/bin/vcfuniq [21:23:53] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:23:53] Found gzip - /bin/gzip [21:23:53] Found vt - /usr/local/bin/vt [21:23:53] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:23:53] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:23:53] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:23:53] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:23:53] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:23:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:23:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:23:54] Please supply a reference FASTA/GBK/EMBL file with --reference
1[21:27:43] This is snippy 4.6.0
Show full stderr[21:27:43] This is snippy 4.6.0 [21:27:43] Written by Torsten Seemann [21:27:43] Obtained from https://github.com/tseemann/snippy [21:27:43] Detected operating system: linux [21:27:43] Enabling bundled linux tools. [21:27:43] Found bwa - /usr/local/bin/bwa [21:27:43] Found bcftools - /usr/local/bin/bcftools [21:27:43] Found samtools - /usr/local/bin/samtools [21:27:43] Found java - /usr/local/bin/java [21:27:43] Found snpEff - /usr/local/bin/snpEff [21:27:43] Found samclip - /usr/local/bin/samclip [21:27:43] Found seqtk - /usr/local/bin/seqtk [21:27:43] Found parallel - /usr/local/bin/parallel [21:27:43] Found freebayes - /usr/local/bin/freebayes [21:27:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:27:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:27:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:27:43] Found vcfuniq - /usr/local/bin/vcfuniq [21:27:43] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:27:43] Found gzip - /bin/gzip [21:27:43] Found vt - /usr/local/bin/vt [21:27:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:27:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:27:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:27:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:27:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:27:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:27:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:27:44] Please supply a reference FASTA/GBK/EMBL file with --reference
1[21:27:50] This is snippy 4.6.0
Show full stderr[21:27:50] This is snippy 4.6.0 [21:27:50] Written by Torsten Seemann [21:27:50] Obtained from https://github.com/tseemann/snippy [21:27:50] Detected operating system: linux [21:27:50] Enabling bundled linux tools. [21:27:50] Found bwa - /usr/local/bin/bwa [21:27:50] Found bcftools - /usr/local/bin/bcftools [21:27:50] Found samtools - /usr/local/bin/samtools [21:27:50] Found java - /usr/local/bin/java [21:27:50] Found snpEff - /usr/local/bin/snpEff [21:27:50] Found samclip - /usr/local/bin/samclip [21:27:50] Found seqtk - /usr/local/bin/seqtk [21:27:50] Found parallel - /usr/local/bin/parallel [21:27:50] Found freebayes - /usr/local/bin/freebayes [21:27:50] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:27:50] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:27:50] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:27:50] Found vcfuniq - /usr/local/bin/vcfuniq [21:27:50] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:27:50] Found gzip - /bin/gzip [21:27:50] Found vt - /usr/local/bin/vt [21:27:50] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:27:50] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:27:51] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:27:51] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:27:51] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:27:51] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:27:51] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:27:51] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:55:39] This is snippy 4.6.0
Show full stderr[01:55:39] This is snippy 4.6.0 [01:55:39] Written by Torsten Seemann [01:55:39] Obtained from https://github.com/tseemann/snippy [01:55:39] Detected operating system: linux [01:55:39] Enabling bundled linux tools. [01:55:39] Found bwa - /usr/local/bin/bwa [01:55:39] Found bcftools - /usr/local/bin/bcftools [01:55:39] Found samtools - /usr/local/bin/samtools [01:55:39] Found java - /usr/local/bin/java [01:55:39] Found snpEff - /usr/local/bin/snpEff [01:55:39] Found samclip - /usr/local/bin/samclip [01:55:39] Found seqtk - /usr/local/bin/seqtk [01:55:39] Found parallel - /usr/local/bin/parallel [01:55:39] Found freebayes - /usr/local/bin/freebayes [01:55:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:55:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:55:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:55:39] Found vcfuniq - /usr/local/bin/vcfuniq [01:55:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:55:39] Found gzip - /bin/gzip [01:55:39] Found vt - /usr/local/bin/vt [01:55:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:55:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:55:40] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:55:40] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:55:40] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:55:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:55:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:55:40] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:58:22] This is snippy 4.6.0
Show full stderr[01:58:22] This is snippy 4.6.0 [01:58:22] Written by Torsten Seemann [01:58:22] Obtained from https://github.com/tseemann/snippy [01:58:22] Detected operating system: linux [01:58:22] Enabling bundled linux tools. [01:58:22] Found bwa - /usr/local/bin/bwa [01:58:22] Found bcftools - /usr/local/bin/bcftools [01:58:22] Found samtools - /usr/local/bin/samtools [01:58:22] Found java - /usr/local/bin/java [01:58:23] Found snpEff - /usr/local/bin/snpEff [01:58:23] Found samclip - /usr/local/bin/samclip [01:58:23] Found seqtk - /usr/local/bin/seqtk [01:58:23] Found parallel - /usr/local/bin/parallel [01:58:23] Found freebayes - /usr/local/bin/freebayes [01:58:23] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:58:23] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:58:23] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:58:23] Found vcfuniq - /usr/local/bin/vcfuniq [01:58:23] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:58:23] Found gzip - /bin/gzip [01:58:23] Found vt - /usr/local/bin/vt [01:58:23] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:58:23] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:58:23] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:58:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:58:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:58:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:58:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:58:23] Please supply a reference FASTA/GBK/EMBL file with --reference
1[06:10:13] This is snippy 4.6.0
Show full stderr[06:10:13] This is snippy 4.6.0 [06:10:13] Written by Torsten Seemann [06:10:13] Obtained from https://github.com/tseemann/snippy [06:10:13] Detected operating system: linux [06:10:13] Enabling bundled linux tools. [06:10:13] Found bwa - /usr/local/bin/bwa [06:10:13] Found bcftools - /usr/local/bin/bcftools [06:10:13] Found samtools - /usr/local/bin/samtools [06:10:13] Found java - /usr/local/bin/java [06:10:13] Found snpEff - /usr/local/bin/snpEff [06:10:14] Found samclip - /usr/local/bin/samclip [06:10:14] Found seqtk - /usr/local/bin/seqtk [06:10:14] Found parallel - /usr/local/bin/parallel [06:10:14] Found freebayes - /usr/local/bin/freebayes [06:10:14] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [06:10:14] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [06:10:14] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [06:10:14] Found vcfuniq - /usr/local/bin/vcfuniq [06:10:14] Found vcffirstheader - /usr/local/bin/vcffirstheader [06:10:14] Found gzip - /bin/gzip [06:10:14] Found vt - /usr/local/bin/vt [06:10:14] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [06:10:14] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [06:10:14] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [06:10:14] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [06:10:14] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [06:10:15] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [06:10:15] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [06:10:15] Using reference: /corral4/main/objects/e/5/8/dataset_e58c24e1-626b-401e-a605-9dc03243b89b.dat [06:10:15] Treating reference as 'genbank' format. [06:10:15] Will use 1 CPU cores. [06:10:15] Using read file: /corral4/main/objects/0/4/d/dataset_04d17ee1-81fe-40d8-912e-65330ca56649.dat [06:10:15] Using read file: /corral4/main/objects/8/3/c/dataset_83c4b454-5c92-43f6-af36-3e60419df6bd.dat [06:10:15] Creating folder: Trimmomatic_on_17EIW9_S21_L001_R1_001_fastq_gz__R1_paired_ [06:10:15] Changing working directory: Trimmomatic_on_17EIW9_S21_L001_R1_001_fastq_gz__R1_paired_ [06:10:15] Creating reference folder: reference [06:10:15] Extracting FASTA and GFF from reference. Use of uninitialized value in uc at /usr/local/bin/snippy line 206, <GEN0> line 84. [06:10:15] Wrote 1 sequences to ref.fa [06:10:15] Wrote 0 features to ref.gff [06:10:15] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time. [06:10:15] Using BAM RG (Read Group) ID: Trimmomatic_on_17EIW9_S21_L001_R1_001_fastq_gz__R1_paired_ [06:10:15] Running: samtools faidx reference/ref.fa 2>> snps.log [06:10:15] Error running command, check Trimmomatic_on_17EIW9_S21_L001_R1_001_fastq_gz__R1_paired_/snps.log
1[02:09:28] This is snippy 4.6.0
Show full stderr[02:09:28] This is snippy 4.6.0 [02:09:28] Written by Torsten Seemann [02:09:28] Obtained from https://github.com/tseemann/snippy [02:09:28] Detected operating system: linux [02:09:28] Enabling bundled linux tools. [02:09:28] Found bwa - /usr/local/bin/bwa [02:09:28] Found bcftools - /usr/local/bin/bcftools [02:09:28] Found samtools - /usr/local/bin/samtools [02:09:28] Found java - /usr/local/bin/java [02:09:28] Found snpEff - /usr/local/bin/snpEff [02:09:28] Found samclip - /usr/local/bin/samclip [02:09:28] Found seqtk - /usr/local/bin/seqtk [02:09:28] Found parallel - /usr/local/bin/parallel [02:09:28] Found freebayes - /usr/local/bin/freebayes [02:09:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [02:09:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [02:09:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [02:09:28] Found vcfuniq - /usr/local/bin/vcfuniq [02:09:28] Found vcffirstheader - /usr/local/bin/vcffirstheader [02:09:28] Found gzip - /bin/gzip [02:09:28] Found vt - /usr/local/bin/vt [02:09:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [02:09:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [02:09:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [02:09:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [02:09:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [02:09:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [02:09:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [02:09:29] Using reference: /corral4/main/objects/b/8/f/dataset_b8fd84bc-39ea-4631-bcf7-cf2275682208.dat [02:09:29] Treating reference as 'genbank' format. [02:09:29] Will use 1 CPU cores. [02:09:29] Using read file: /corral4/main/objects/d/1/9/dataset_d198d016-bd24-4ea3-a2cb-969dbc125b01.dat [02:09:29] Using read file: /corral4/main/objects/2/9/c/dataset_29c0f420-3e0c-4496-a95c-04d629204009.dat [02:09:29] Creating folder: Trim_Galore__on_dataset_1_and_2__trimmed_reads_pair_1 [02:09:29] Changing working directory: Trim_Galore__on_dataset_1_and_2__trimmed_reads_pair_1 [02:09:29] Creating reference folder: reference [02:09:29] Extracting FASTA and GFF from reference. [02:09:32] Wrote 1 sequences to ref.fa [02:09:32] Wrote 5017 features to ref.gff [02:09:32] Creating reference/snpeff.config [02:09:32] Freebayes will process 1 chunks of 1000 bp, 1 chunks at a time. [02:09:32] Using BAM RG (Read Group) ID: Trim_Galore__on_dataset_1_and_2__trimmed_reads_pair_1 [02:09:32] Running: samtools faidx reference/ref.fa 2>> snps.log [02:09:32] Error running command, check Trim_Galore__on_dataset_1_and_2__trimmed_reads_pair_1/snps.log
1[07:42:58] This is snippy 4.6.0
Show full stderr[07:42:58] This is snippy 4.6.0 [07:42:58] Written by Torsten Seemann [07:42:58] Obtained from https://github.com/tseemann/snippy [07:42:58] Detected operating system: linux [07:42:58] Enabling bundled linux tools. [07:42:58] Found bwa - /usr/local/bin/bwa [07:42:58] Found bcftools - /usr/local/bin/bcftools [07:42:58] Found samtools - /usr/local/bin/samtools [07:42:58] Found java - /usr/local/bin/java [07:42:58] Found snpEff - /usr/local/bin/snpEff [07:42:58] Found samclip - /usr/local/bin/samclip [07:42:58] Found seqtk - /usr/local/bin/seqtk [07:42:58] Found parallel - /usr/local/bin/parallel [07:42:58] Found freebayes - /usr/local/bin/freebayes [07:42:58] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:42:58] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:42:58] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:42:58] Found vcfuniq - /usr/local/bin/vcfuniq [07:42:58] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:42:58] Found gzip - /bin/gzip [07:42:58] Found vt - /usr/local/bin/vt [07:42:58] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:42:58] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:42:58] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:42:58] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:42:59] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:42:59] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:42:59] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:42:59] Please supply a reference FASTA/GBK/EMBL file with --reference
1[11:35:07] This is snippy 4.6.0
Show full stderr[11:35:07] This is snippy 4.6.0 [11:35:07] Written by Torsten Seemann [11:35:07] Obtained from https://github.com/tseemann/snippy [11:35:07] Detected operating system: linux [11:35:07] Enabling bundled linux tools. [11:35:07] Found bwa - /usr/local/bin/bwa [11:35:07] Found bcftools - /usr/local/bin/bcftools [11:35:07] Found samtools - /usr/local/bin/samtools [11:35:07] Found java - /usr/local/bin/java [11:35:07] Found snpEff - /usr/local/bin/snpEff [11:35:07] Found samclip - /usr/local/bin/samclip [11:35:07] Found seqtk - /usr/local/bin/seqtk [11:35:07] Found parallel - /usr/local/bin/parallel [11:35:07] Found freebayes - /usr/local/bin/freebayes [11:35:07] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [11:35:07] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [11:35:07] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [11:35:07] Found vcfuniq - /usr/local/bin/vcfuniq [11:35:07] Found vcffirstheader - /usr/local/bin/vcffirstheader [11:35:07] Found gzip - /bin/gzip [11:35:07] Found vt - /usr/local/bin/vt [11:35:07] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [11:35:07] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [11:35:07] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [11:35:07] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [11:35:08] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [11:35:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [11:35:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [11:35:08] Please supply a reference FASTA/GBK/EMBL file with --reference
1[11:35:49] This is snippy 4.6.0
Show full stderr[11:35:49] This is snippy 4.6.0 [11:35:49] Written by Torsten Seemann [11:35:49] Obtained from https://github.com/tseemann/snippy [11:35:49] Detected operating system: linux [11:35:49] Enabling bundled linux tools. [11:35:49] Found bwa - /usr/local/bin/bwa [11:35:49] Found bcftools - /usr/local/bin/bcftools [11:35:49] Found samtools - /usr/local/bin/samtools [11:35:49] Found java - /usr/local/bin/java [11:35:49] Found snpEff - /usr/local/bin/snpEff [11:35:49] Found samclip - /usr/local/bin/samclip [11:35:49] Found seqtk - /usr/local/bin/seqtk [11:35:49] Found parallel - /usr/local/bin/parallel [11:35:49] Found freebayes - /usr/local/bin/freebayes [11:35:49] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [11:35:49] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [11:35:49] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [11:35:49] Found vcfuniq - /usr/local/bin/vcfuniq [11:35:49] Found vcffirstheader - /usr/local/bin/vcffirstheader [11:35:49] Found gzip - /bin/gzip [11:35:49] Found vt - /usr/local/bin/vt [11:35:49] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [11:35:49] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [11:35:49] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [11:35:49] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [11:35:49] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [11:35:50] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [11:35:50] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [11:35:50] Please supply a reference FASTA/GBK/EMBL file with --reference
1[11:36:38] This is snippy 4.6.0
Show full stderr[11:36:38] This is snippy 4.6.0 [11:36:38] Written by Torsten Seemann [11:36:38] Obtained from https://github.com/tseemann/snippy [11:36:38] Detected operating system: linux [11:36:38] Enabling bundled linux tools. [11:36:38] Found bwa - /usr/local/bin/bwa [11:36:38] Found bcftools - /usr/local/bin/bcftools [11:36:38] Found samtools - /usr/local/bin/samtools [11:36:38] Found java - /usr/local/bin/java [11:36:38] Found snpEff - /usr/local/bin/snpEff [11:36:38] Found samclip - /usr/local/bin/samclip [11:36:38] Found seqtk - /usr/local/bin/seqtk [11:36:38] Found parallel - /usr/local/bin/parallel [11:36:38] Found freebayes - /usr/local/bin/freebayes [11:36:38] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [11:36:38] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [11:36:38] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [11:36:38] Found vcfuniq - /usr/local/bin/vcfuniq [11:36:38] Found vcffirstheader - /usr/local/bin/vcffirstheader [11:36:38] Found gzip - /bin/gzip [11:36:38] Found vt - /usr/local/bin/vt [11:36:38] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [11:36:38] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [11:36:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [11:36:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [11:36:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [11:36:39] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [11:36:39] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [11:36:39] Please supply a reference FASTA/GBK/EMBL file with --reference
1[11:37:20] This is snippy 4.6.0
Show full stderr[11:37:20] This is snippy 4.6.0 [11:37:20] Written by Torsten Seemann [11:37:20] Obtained from https://github.com/tseemann/snippy [11:37:20] Detected operating system: linux [11:37:20] Enabling bundled linux tools. [11:37:20] Found bwa - /usr/local/bin/bwa [11:37:20] Found bcftools - /usr/local/bin/bcftools [11:37:20] Found samtools - /usr/local/bin/samtools [11:37:20] Found java - /usr/local/bin/java [11:37:20] Found snpEff - /usr/local/bin/snpEff [11:37:20] Found samclip - /usr/local/bin/samclip [11:37:20] Found seqtk - /usr/local/bin/seqtk [11:37:20] Found parallel - /usr/local/bin/parallel [11:37:20] Found freebayes - /usr/local/bin/freebayes [11:37:20] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [11:37:20] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [11:37:20] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [11:37:20] Found vcfuniq - /usr/local/bin/vcfuniq [11:37:20] Found vcffirstheader - /usr/local/bin/vcffirstheader [11:37:20] Found gzip - /bin/gzip [11:37:20] Found vt - /usr/local/bin/vt [11:37:20] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [11:37:20] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [11:37:21] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [11:37:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [11:37:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [11:37:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [11:37:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [11:37:21] Please supply a reference FASTA/GBK/EMBL file with --reference
1[14:15:28] This is snippy 4.6.0
Show full stderr[14:15:28] This is snippy 4.6.0 [14:15:28] Written by Torsten Seemann [14:15:28] Obtained from https://github.com/tseemann/snippy [14:15:28] Detected operating system: linux [14:15:28] Enabling bundled linux tools. [14:15:28] Found bwa - /usr/local/bin/bwa [14:15:28] Found bcftools - /usr/local/bin/bcftools [14:15:28] Found samtools - /usr/local/bin/samtools [14:15:28] Found java - /usr/local/bin/java [14:15:28] Found snpEff - /usr/local/bin/snpEff [14:15:28] Found samclip - /usr/local/bin/samclip [14:15:28] Found seqtk - /usr/local/bin/seqtk [14:15:28] Found parallel - /usr/local/bin/parallel [14:15:28] Found freebayes - /usr/local/bin/freebayes [14:15:28] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [14:15:28] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [14:15:28] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [14:15:28] Found vcfuniq - /usr/local/bin/vcfuniq [14:15:28] Found vcffirstheader - /usr/local/bin/vcffirstheader [14:15:28] Found gzip - /bin/gzip [14:15:28] Found vt - /usr/local/bin/vt [14:15:28] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [14:15:28] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [14:15:28] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [14:15:28] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [14:15:28] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:15:29] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:15:29] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:15:29] Using reference: /corral4/main/objects/b/c/6/dataset_bc64c99a-098a-4a41-9acd-d60322a2c629.dat [14:15:29] Treating reference as 'fasta' format. [14:15:29] Will use 1 CPU cores. [14:15:29] Using read file: /corral4/main/objects/c/1/4/dataset_c1497bab-6824-4297-86c0-caec26b178f0.dat [14:15:29] Using read file: /corral4/main/objects/2/0/0/dataset_200e2f81-1b65-4350-90e3-3d01c6420d58.dat [14:15:29] Creating folder: 317753_A2_1_trimmed_fastq_gz [14:15:29] Changing working directory: 317753_A2_1_trimmed_fastq_gz [14:15:29] Creating reference folder: reference [14:15:29] Extracting FASTA and GFF from reference. [14:15:29] Duplicate sequence PGD104247 in /corral4/main/objects/b/c/6/dataset_bc64c99a-098a-4a41-9acd-d60322a2c629.dat
1[21:39:12] This is snippy 4.6.0
Show full stderr[21:39:12] This is snippy 4.6.0 [21:39:12] Written by Torsten Seemann [21:39:12] Obtained from https://github.com/tseemann/snippy [21:39:12] Detected operating system: linux [21:39:12] Enabling bundled linux tools. [21:39:12] Found bwa - /usr/local/bin/bwa [21:39:12] Found bcftools - /usr/local/bin/bcftools [21:39:12] Found samtools - /usr/local/bin/samtools [21:39:12] Found java - /usr/local/bin/java [21:39:12] Found snpEff - /usr/local/bin/snpEff [21:39:12] Found samclip - /usr/local/bin/samclip [21:39:12] Found seqtk - /usr/local/bin/seqtk [21:39:12] Found parallel - /usr/local/bin/parallel [21:39:12] Found freebayes - /usr/local/bin/freebayes [21:39:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [21:39:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [21:39:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [21:39:12] Found vcfuniq - /usr/local/bin/vcfuniq [21:39:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [21:39:12] Found gzip - /bin/gzip [21:39:12] Found vt - /usr/local/bin/vt [21:39:13] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [21:39:13] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [21:39:13] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [21:39:13] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [21:39:13] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [21:39:14] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:39:14] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [21:39:14] Using reference: /corral4/main/objects/6/0/2/dataset_6023055f-9028-43b4-93e3-88a86498afa1.dat [21:39:16] Treating reference as 'genbank' format. [21:39:16] Will use 1 CPU cores. [21:39:16] Using read file: /corral4/main/objects/a/5/3/dataset_a5387cee-8bf5-436d-a74c-21634876c586.dat [21:39:16] Using read file: /corral4/main/objects/0/3/6/dataset_03698956-ef1e-40c3-9bed-675afa86f1c3.dat [21:39:16] Creating folder: SRR29263914 [21:39:16] Changing working directory: SRR29263914 [21:39:16] Creating reference folder: reference [21:39:17] Extracting FASTA and GFF from reference. --------------------- WARNING --------------------- MSG: Bad LOCUS name? Changing [NODE_1_length_657186_cov_100.680931657186] to 'unknown' and length to 'NODE_1_length_657186_cov_100.680931657186' --------------------------------------------------- --------------------- WARNING --------------------- MSG: Bad LOCUS name? Changing [NODE_2_length_636502_cov_103.943722636502] to 'unknown' and length to 'NODE_2_length_636502_cov_103.943722636502' --------------------------------------------------- [21:39:17] Duplicate sequence unknown in /corral4/main/objects/6/0/2/dataset_6023055f-9028-43b4-93e3-88a86498afa1.dat
1[22:01:43] This is snippy 4.6.0
Show full stderr[22:01:43] This is snippy 4.6.0 [22:01:43] Written by Torsten Seemann [22:01:43] Obtained from https://github.com/tseemann/snippy [22:01:43] Detected operating system: linux [22:01:43] Enabling bundled linux tools. [22:01:43] Found bwa - /usr/local/bin/bwa [22:01:43] Found bcftools - /usr/local/bin/bcftools [22:01:43] Found samtools - /usr/local/bin/samtools [22:01:43] Found java - /usr/local/bin/java [22:01:43] Found snpEff - /usr/local/bin/snpEff [22:01:43] Found samclip - /usr/local/bin/samclip [22:01:43] Found seqtk - /usr/local/bin/seqtk [22:01:43] Found parallel - /usr/local/bin/parallel [22:01:43] Found freebayes - /usr/local/bin/freebayes [22:01:43] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [22:01:43] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [22:01:43] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [22:01:43] Found vcfuniq - /usr/local/bin/vcfuniq [22:01:43] Found vcffirstheader - /usr/local/bin/vcffirstheader [22:01:43] Found gzip - /bin/gzip [22:01:43] Found vt - /usr/local/bin/vt [22:01:43] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [22:01:43] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [22:01:43] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [22:01:43] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [22:01:43] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [22:01:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [22:01:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [22:01:44] Using reference: /corral4/main/objects/9/c/a/dataset_9cabf3b6-e6d3-4dcd-8e07-292b26f608af.dat [22:01:44] Treating reference as 'fasta' format. [22:01:44] Will use 1 CPU cores. [22:01:44] Using read file: /corral4/main/objects/1/d/7/dataset_1d7bb7d9-1fb9-4358-b904-2d372d1dc701.dat [22:01:44] Using read file: /corral4/main/objects/6/4/0/dataset_6403a9a4-acfb-454f-b397-c408c55b4140.dat [22:01:44] Creating folder: SRR12131097 [22:01:44] Changing working directory: SRR12131097 [22:01:44] Creating reference folder: reference [22:01:44] Extracting FASTA and GFF from reference. [22:01:45] Wrote 4 sequences to ref.fa [22:01:45] Wrote 0 features to ref.gff [22:01:45] Freebayes will process 1 chunks of 6687074 bp, 1 chunks at a time. [22:01:45] Using BAM RG (Read Group) ID: SRR12131097 [22:01:45] Running: samtools faidx reference/ref.fa 2>> snps.log [22:01:45] Running: bwa index reference/ref.fa 2>> snps.log [22:01:52] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [22:01:52] Running: ln -sf reference/ref.fa . 2>> snps.log [22:01:52] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [22:01:53] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [22:01:53] Running: bwa mem -Y -M -R '@RG\tID:SRR12131097\tSM:SRR12131097' -t 1 reference/ref.fa /corral4/main/objects/1/d/7/dataset_1d7bb7d9-1fb9-4358-b904-2d372d1dc701.dat /corral4/main/objects/6/4/0/dataset_6403a9a4-acfb-454f-b397-c408c55b4140.dat | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /corral4/main/jobs/073/225/73225392/tmp --threads 0 -m 12000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /corral4/main/jobs/073/225/73225392/tmp --threads 0 -m 12000M | samtools markdup -T /corral4/main/jobs/073/225/73225392/tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 4 sequences in reference/ref.fa.fai [M::pro
1[23:59:17] This is snippy 4.6.0
Show full stderr[23:59:17] This is snippy 4.6.0 [23:59:17] Written by Torsten Seemann [23:59:17] Obtained from https://github.com/tseemann/snippy [23:59:17] Detected operating system: linux [23:59:17] Enabling bundled linux tools. [23:59:17] Found bwa - /usr/local/bin/bwa [23:59:17] Found bcftools - /usr/local/bin/bcftools [23:59:17] Found samtools - /usr/local/bin/samtools [23:59:17] Found java - /usr/local/bin/java [23:59:17] Found snpEff - /usr/local/bin/snpEff [23:59:17] Found samclip - /usr/local/bin/samclip [23:59:17] Found seqtk - /usr/local/bin/seqtk [23:59:17] Found parallel - /usr/local/bin/parallel [23:59:17] Found freebayes - /usr/local/bin/freebayes [23:59:17] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [23:59:17] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [23:59:17] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [23:59:17] Found vcfuniq - /usr/local/bin/vcfuniq [23:59:17] Found vcffirstheader - /usr/local/bin/vcffirstheader [23:59:17] Found gzip - /bin/gzip [23:59:17] Found vt - /usr/local/bin/vt [23:59:17] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [23:59:17] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [23:59:17] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [23:59:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [23:59:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [23:59:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [23:59:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [23:59:17] Using reference: /corral4/main/objects/2/e/1/dataset_2e11e81e-1139-4b27-a8be-8b1907183159.dat [23:59:18] Treating reference as 'genbank' format. [23:59:18] Will use 1 CPU cores. [23:59:18] Using read file: /corral4/main/objects/e/d/2/dataset_ed2636a4-201d-496a-a51b-89a76b9503c8.dat [23:59:18] Using read file: /corral4/main/objects/8/3/6/dataset_836031cd-336f-451b-af07-41dd1df77396.dat [23:59:18] Creating folder: Trim_Galore__on_dataset_1_and_2__trimmed_reads_pair_1 [23:59:18] Changing working directory: Trim_Galore__on_dataset_1_and_2__trimmed_reads_pair_1 [23:59:18] Creating reference folder: reference [23:59:18] Extracting FASTA and GFF from reference. [23:59:31] Wrote 4901 sequences to ref.fa [23:59:31] Wrote 4901 features to ref.gff [23:59:31] Creating reference/snpeff.config [23:59:31] Freebayes will process 1 chunks of 1944614 bp, 1 chunks at a time. [23:59:31] Using BAM RG (Read Group) ID: Trim_Galore__on_dataset_1_and_2__trimmed_reads_pair_1 [23:59:31] Running: samtools faidx reference/ref.fa 2>> snps.log [23:59:31] Running: bwa index reference/ref.fa 2>> snps.log [23:59:32] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [23:59:32] Running: ln -sf reference/ref.fa . 2>> snps.log [23:59:32] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [23:59:32] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [23:59:32] Running: snpEff build -c reference/snpeff.config -dataDir . -gff3 ref 2>> snps.log [23:59:41] Error running command, check Trim_Galore__on_dataset_1_and_2__trimmed_reads_pair_1/snps.log
1[00:12:59] This is snippy 4.6.0
Show full stderr[00:12:59] This is snippy 4.6.0 [00:12:59] Written by Torsten Seemann [00:12:59] Obtained from https://github.com/tseemann/snippy [00:12:59] Detected operating system: linux [00:12:59] Enabling bundled linux tools. [00:12:59] Found bwa - /usr/local/bin/bwa [00:12:59] Found bcftools - /usr/local/bin/bcftools [00:12:59] Found samtools - /usr/local/bin/samtools [00:12:59] Found java - /usr/local/bin/java [00:12:59] Found snpEff - /usr/local/bin/snpEff [00:12:59] Found samclip - /usr/local/bin/samclip [00:12:59] Found seqtk - /usr/local/bin/seqtk [00:12:59] Found parallel - /usr/local/bin/parallel [00:12:59] Found freebayes - /usr/local/bin/freebayes [00:12:59] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:12:59] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:12:59] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:12:59] Found vcfuniq - /usr/local/bin/vcfuniq [00:12:59] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:12:59] Found gzip - /bin/gzip [00:12:59] Found vt - /usr/local/bin/vt [00:12:59] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:12:59] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:13:00] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:13:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:13:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:13:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:13:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:13:00] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:18:16] This is snippy 4.6.0
Show full stderr[00:18:16] This is snippy 4.6.0 [00:18:16] Written by Torsten Seemann [00:18:16] Obtained from https://github.com/tseemann/snippy [00:18:16] Detected operating system: linux [00:18:16] Enabling bundled linux tools. [00:18:16] Found bwa - /usr/local/bin/bwa [00:18:16] Found bcftools - /usr/local/bin/bcftools [00:18:16] Found samtools - /usr/local/bin/samtools [00:18:16] Found java - /usr/local/bin/java [00:18:16] Found snpEff - /usr/local/bin/snpEff [00:18:16] Found samclip - /usr/local/bin/samclip [00:18:16] Found seqtk - /usr/local/bin/seqtk [00:18:16] Found parallel - /usr/local/bin/parallel [00:18:16] Found freebayes - /usr/local/bin/freebayes [00:18:16] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:18:16] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:18:16] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:18:16] Found vcfuniq - /usr/local/bin/vcfuniq [00:18:16] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:18:16] Found gzip - /bin/gzip [00:18:16] Found vt - /usr/local/bin/vt [00:18:16] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:18:16] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:18:16] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:18:16] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:18:16] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:18:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:18:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:18:17] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:20:15] This is snippy 4.6.0
Show full stderr[00:20:15] This is snippy 4.6.0 [00:20:15] Written by Torsten Seemann [00:20:15] Obtained from https://github.com/tseemann/snippy [00:20:15] Detected operating system: linux [00:20:15] Enabling bundled linux tools. [00:20:15] Found bwa - /usr/local/bin/bwa [00:20:15] Found bcftools - /usr/local/bin/bcftools [00:20:15] Found samtools - /usr/local/bin/samtools [00:20:15] Found java - /usr/local/bin/java [00:20:15] Found snpEff - /usr/local/bin/snpEff [00:20:15] Found samclip - /usr/local/bin/samclip [00:20:15] Found seqtk - /usr/local/bin/seqtk [00:20:15] Found parallel - /usr/local/bin/parallel [00:20:15] Found freebayes - /usr/local/bin/freebayes [00:20:15] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:20:15] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:20:15] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:20:15] Found vcfuniq - /usr/local/bin/vcfuniq [00:20:15] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:20:15] Found gzip - /bin/gzip [00:20:15] Found vt - /usr/local/bin/vt [00:20:15] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:20:15] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:20:15] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:20:15] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:20:15] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:20:16] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:20:16] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:20:16] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:45:11] This is snippy 4.6.0
Show full stderr[00:45:11] This is snippy 4.6.0 [00:45:11] Written by Torsten Seemann [00:45:11] Obtained from https://github.com/tseemann/snippy [00:45:11] Detected operating system: linux [00:45:11] Enabling bundled linux tools. [00:45:11] Found bwa - /usr/local/bin/bwa [00:45:11] Found bcftools - /usr/local/bin/bcftools [00:45:11] Found samtools - /usr/local/bin/samtools [00:45:11] Found java - /usr/local/bin/java [00:45:11] Found snpEff - /usr/local/bin/snpEff [00:45:11] Found samclip - /usr/local/bin/samclip [00:45:11] Found seqtk - /usr/local/bin/seqtk [00:45:11] Found parallel - /usr/local/bin/parallel [00:45:11] Found freebayes - /usr/local/bin/freebayes [00:45:11] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:45:11] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:45:11] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:45:11] Found vcfuniq - /usr/local/bin/vcfuniq [00:45:11] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:45:11] Found gzip - /bin/gzip [00:45:11] Found vt - /usr/local/bin/vt [00:45:11] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:45:11] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:45:11] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:45:11] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:45:11] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:45:12] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:45:12] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:45:12] Please supply a reference FASTA/GBK/EMBL file with --reference
1[00:55:40] This is snippy 4.6.0
Show full stderr[00:55:40] This is snippy 4.6.0 [00:55:40] Written by Torsten Seemann [00:55:40] Obtained from https://github.com/tseemann/snippy [00:55:40] Detected operating system: linux [00:55:40] Enabling bundled linux tools. [00:55:40] Found bwa - /usr/local/bin/bwa [00:55:40] Found bcftools - /usr/local/bin/bcftools [00:55:40] Found samtools - /usr/local/bin/samtools [00:55:40] Found java - /usr/local/bin/java [00:55:40] Found snpEff - /usr/local/bin/snpEff [00:55:40] Found samclip - /usr/local/bin/samclip [00:55:40] Found seqtk - /usr/local/bin/seqtk [00:55:40] Found parallel - /usr/local/bin/parallel [00:55:40] Found freebayes - /usr/local/bin/freebayes [00:55:40] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [00:55:40] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [00:55:40] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [00:55:40] Found vcfuniq - /usr/local/bin/vcfuniq [00:55:40] Found vcffirstheader - /usr/local/bin/vcffirstheader [00:55:40] Found gzip - /bin/gzip [00:55:40] Found vt - /usr/local/bin/vt [00:55:40] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [00:55:40] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [00:55:41] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [00:55:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [00:55:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [00:55:42] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [00:55:42] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [00:55:42] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:04:46] This is snippy 4.6.0
Show full stderr[01:04:46] This is snippy 4.6.0 [01:04:46] Written by Torsten Seemann [01:04:46] Obtained from https://github.com/tseemann/snippy [01:04:46] Detected operating system: linux [01:04:46] Enabling bundled linux tools. [01:04:46] Found bwa - /usr/local/bin/bwa [01:04:46] Found bcftools - /usr/local/bin/bcftools [01:04:46] Found samtools - /usr/local/bin/samtools [01:04:46] Found java - /usr/local/bin/java [01:04:46] Found snpEff - /usr/local/bin/snpEff [01:04:46] Found samclip - /usr/local/bin/samclip [01:04:46] Found seqtk - /usr/local/bin/seqtk [01:04:46] Found parallel - /usr/local/bin/parallel [01:04:46] Found freebayes - /usr/local/bin/freebayes [01:04:46] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:04:46] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:04:46] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:04:46] Found vcfuniq - /usr/local/bin/vcfuniq [01:04:46] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:04:46] Found gzip - /bin/gzip [01:04:46] Found vt - /usr/local/bin/vt [01:04:47] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:04:47] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:04:47] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:04:47] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:04:47] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:04:48] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:04:48] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:04:48] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:08:19] This is snippy 4.6.0
Show full stderr[01:08:19] This is snippy 4.6.0 [01:08:19] Written by Torsten Seemann [01:08:19] Obtained from https://github.com/tseemann/snippy [01:08:19] Detected operating system: linux [01:08:19] Enabling bundled linux tools. [01:08:19] Found bwa - /usr/local/bin/bwa [01:08:19] Found bcftools - /usr/local/bin/bcftools [01:08:19] Found samtools - /usr/local/bin/samtools [01:08:19] Found java - /usr/local/bin/java [01:08:19] Found snpEff - /usr/local/bin/snpEff [01:08:19] Found samclip - /usr/local/bin/samclip [01:08:19] Found seqtk - /usr/local/bin/seqtk [01:08:19] Found parallel - /usr/local/bin/parallel [01:08:19] Found freebayes - /usr/local/bin/freebayes [01:08:19] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:08:19] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:08:19] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:08:19] Found vcfuniq - /usr/local/bin/vcfuniq [01:08:19] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:08:19] Found gzip - /bin/gzip [01:08:19] Found vt - /usr/local/bin/vt [01:08:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:08:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:08:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:08:20] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:08:20] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:08:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:08:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:08:20] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:12:29] This is snippy 4.6.0
Show full stderr[01:12:29] This is snippy 4.6.0 [01:12:29] Written by Torsten Seemann [01:12:29] Obtained from https://github.com/tseemann/snippy [01:12:29] Detected operating system: linux [01:12:29] Enabling bundled linux tools. [01:12:29] Found bwa - /usr/local/bin/bwa [01:12:29] Found bcftools - /usr/local/bin/bcftools [01:12:29] Found samtools - /usr/local/bin/samtools [01:12:29] Found java - /usr/local/bin/java [01:12:29] Found snpEff - /usr/local/bin/snpEff [01:12:29] Found samclip - /usr/local/bin/samclip [01:12:29] Found seqtk - /usr/local/bin/seqtk [01:12:29] Found parallel - /usr/local/bin/parallel [01:12:29] Found freebayes - /usr/local/bin/freebayes [01:12:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:12:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:12:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:12:29] Found vcfuniq - /usr/local/bin/vcfuniq [01:12:29] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:12:29] Found gzip - /bin/gzip [01:12:29] Found vt - /usr/local/bin/vt [01:12:29] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:12:29] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:12:29] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:12:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:12:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:12:36] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:12:36] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:12:36] Please supply a reference FASTA/GBK/EMBL file with --reference
1[01:35:09] This is snippy 4.6.0
Show full stderr[01:35:09] This is snippy 4.6.0 [01:35:09] Written by Torsten Seemann [01:35:09] Obtained from https://github.com/tseemann/snippy [01:35:09] Detected operating system: linux [01:35:09] Enabling bundled linux tools. [01:35:09] Found bwa - /usr/local/bin/bwa [01:35:09] Found bcftools - /usr/local/bin/bcftools [01:35:09] Found samtools - /usr/local/bin/samtools [01:35:09] Found java - /usr/local/bin/java [01:35:09] Found snpEff - /usr/local/bin/snpEff [01:35:09] Found samclip - /usr/local/bin/samclip [01:35:09] Found seqtk - /usr/local/bin/seqtk [01:35:09] Found parallel - /usr/local/bin/parallel [01:35:09] Found freebayes - /usr/local/bin/freebayes [01:35:09] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:35:09] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:35:09] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:35:09] Found vcfuniq - /usr/local/bin/vcfuniq [01:35:09] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:35:10] Found gzip - /bin/gzip [01:35:10] Found vt - /usr/local/bin/vt [01:35:10] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:35:10] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:35:10] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:35:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:35:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:35:11] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:35:11] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:35:11] Using reference: /corral4/main/objects/9/e/0/dataset_9e02d4cd-cefb-4d60-bdfe-8d8d5dc517e2.dat [01:35:11] Treating reference as 'genbank' format. [01:35:11] Will use 1 CPU cores. [01:35:11] Using read file: /corral4/main/objects/0/6/d/dataset_06ddbb48-7021-4b41-9eef-763850e97837.dat [01:35:11] Creating folder: SPAdes_on_dataset_11_and_12_and_collection_9__Contigs [01:35:11] Changing working directory: SPAdes_on_dataset_11_and_12_and_collection_9__Contigs [01:35:11] Creating reference folder: reference [01:35:11] Extracting FASTA and GFF from reference. --------------------- WARNING --------------------- MSG: Bad LOCUS name? Changing [NODE_1_length_657186_cov_83.784211657186] to 'unknown' and length to 'NODE_1_length_657186_cov_83.784211657186' --------------------------------------------------- --------------------- WARNING --------------------- MSG: Bad LOCUS name? Changing [NODE_2_length_642178_cov_95.522608642178] to 'unknown' and length to 'NODE_2_length_642178_cov_95.522608642178' --------------------------------------------------- [01:35:12] Duplicate sequence unknown in /corral4/main/objects/9/e/0/dataset_9e02d4cd-cefb-4d60-bdfe-8d8d5dc517e2.dat
1[01:41:29] This is snippy 4.6.0
Show full stderr[01:41:29] This is snippy 4.6.0 [01:41:29] Written by Torsten Seemann [01:41:29] Obtained from https://github.com/tseemann/snippy [01:41:29] Detected operating system: linux [01:41:29] Enabling bundled linux tools. [01:41:29] Found bwa - /usr/local/bin/bwa [01:41:29] Found bcftools - /usr/local/bin/bcftools [01:41:29] Found samtools - /usr/local/bin/samtools [01:41:29] Found java - /usr/local/bin/java [01:41:29] Found snpEff - /usr/local/bin/snpEff [01:41:29] Found samclip - /usr/local/bin/samclip [01:41:29] Found seqtk - /usr/local/bin/seqtk [01:41:29] Found parallel - /usr/local/bin/parallel [01:41:29] Found freebayes - /usr/local/bin/freebayes [01:41:29] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:41:29] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:41:29] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:41:29] Found vcfuniq - /usr/local/bin/vcfuniq [01:41:29] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:41:29] Found gzip - /bin/gzip [01:41:29] Found vt - /usr/local/bin/vt [01:41:29] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:41:29] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:41:29] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:41:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:41:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:41:30] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:41:30] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:41:30] Using reference: /corral4/main/objects/f/b/5/dataset_fb57894d-62c4-4c95-aa14-2565ed9bd238.dat [01:41:30] Treating reference as 'genbank' format. [01:41:30] Will use 1 CPU cores. [01:41:30] Using read file: /corral4/main/objects/4/8/3/dataset_4836aced-4bf9-4447-8ad6-c801870ffaae.dat [01:41:30] Using read file: /corral4/main/objects/5/a/4/dataset_5a409afa-8107-4217-bc19-eb4adc63ad1e.dat [01:41:30] Creating folder: SRR29263912 [01:41:30] Changing working directory: SRR29263912 [01:41:30] Creating reference folder: reference [01:41:30] Extracting FASTA and GFF from reference. --------------------- WARNING --------------------- MSG: Bad LOCUS name? Changing [NODE_1_length_657186_cov_100.680931657186] to 'unknown' and length to 'NODE_1_length_657186_cov_100.680931657186' --------------------------------------------------- --------------------- WARNING --------------------- MSG: Bad LOCUS name? Changing [NODE_2_length_642180_cov_109.339456642180] to 'unknown' and length to 'NODE_2_length_642180_cov_109.339456642180' --------------------------------------------------- [01:41:31] Duplicate sequence unknown in /corral4/main/objects/f/b/5/dataset_fb57894d-62c4-4c95-aa14-2565ed9bd238.dat
1[01:56:36] This is snippy 4.6.0
Show full stderr[01:56:36] This is snippy 4.6.0 [01:56:36] Written by Torsten Seemann [01:56:36] Obtained from https://github.com/tseemann/snippy [01:56:36] Detected operating system: linux [01:56:36] Enabling bundled linux tools. [01:56:36] Found bwa - /usr/local/bin/bwa [01:56:36] Found bcftools - /usr/local/bin/bcftools [01:56:37] Found samtools - /usr/local/bin/samtools [01:56:37] Found java - /usr/local/bin/java [01:56:37] Found snpEff - /usr/local/bin/snpEff [01:56:37] Found samclip - /usr/local/bin/samclip [01:56:37] Found seqtk - /usr/local/bin/seqtk [01:56:37] Found parallel - /usr/local/bin/parallel [01:56:37] Found freebayes - /usr/local/bin/freebayes [01:56:37] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [01:56:37] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [01:56:37] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [01:56:37] Found vcfuniq - /usr/local/bin/vcfuniq [01:56:37] Found vcffirstheader - /usr/local/bin/vcffirstheader [01:56:37] Found gzip - /bin/gzip [01:56:37] Found vt - /usr/local/bin/vt [01:56:37] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [01:56:37] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [01:56:37] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [01:56:37] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [01:56:37] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [01:56:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [01:56:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [01:56:38] Please supply a reference FASTA/GBK/EMBL file with --reference
1[03:59:12] This is snippy 4.6.0
Show full stderr[03:59:12] This is snippy 4.6.0 [03:59:12] Written by Torsten Seemann [03:59:12] Obtained from https://github.com/tseemann/snippy [03:59:12] Detected operating system: linux [03:59:12] Enabling bundled linux tools. [03:59:12] Found bwa - /usr/local/bin/bwa [03:59:12] Found bcftools - /usr/local/bin/bcftools [03:59:12] Found samtools - /usr/local/bin/samtools [03:59:12] Found java - /usr/local/bin/java [03:59:12] Found snpEff - /usr/local/bin/snpEff [03:59:12] Found samclip - /usr/local/bin/samclip [03:59:12] Found seqtk - /usr/local/bin/seqtk [03:59:12] Found parallel - /usr/local/bin/parallel [03:59:12] Found freebayes - /usr/local/bin/freebayes [03:59:12] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:59:12] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:59:12] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:59:12] Found vcfuniq - /usr/local/bin/vcfuniq [03:59:12] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:59:12] Found gzip - /bin/gzip [03:59:12] Found vt - /usr/local/bin/vt [03:59:12] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:59:12] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:59:12] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:59:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:59:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:59:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:59:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:59:13] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:02:18] This is snippy 4.6.0
Show full stderr[05:02:18] This is snippy 4.6.0 [05:02:18] Written by Torsten Seemann [05:02:18] Obtained from https://github.com/tseemann/snippy [05:02:18] Detected operating system: linux [05:02:18] Enabling bundled linux tools. [05:02:18] Found bwa - /usr/local/bin/bwa [05:02:18] Found bcftools - /usr/local/bin/bcftools [05:02:18] Found samtools - /usr/local/bin/samtools [05:02:18] Found java - /usr/local/bin/java [05:02:18] Found snpEff - /usr/local/bin/snpEff [05:02:18] Found samclip - /usr/local/bin/samclip [05:02:18] Found seqtk - /usr/local/bin/seqtk [05:02:18] Found parallel - /usr/local/bin/parallel [05:02:18] Found freebayes - /usr/local/bin/freebayes [05:02:18] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:02:18] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:02:18] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:02:18] Found vcfuniq - /usr/local/bin/vcfuniq [05:02:18] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:02:18] Found gzip - /bin/gzip [05:02:18] Found vt - /usr/local/bin/vt [05:02:19] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:02:19] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:02:19] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:02:19] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:02:19] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:02:20] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:02:20] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:02:20] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:04:54] This is snippy 4.6.0
Show full stderr[05:04:54] This is snippy 4.6.0 [05:04:54] Written by Torsten Seemann [05:04:54] Obtained from https://github.com/tseemann/snippy [05:04:54] Detected operating system: linux [05:04:54] Enabling bundled linux tools. [05:04:54] Found bwa - /usr/local/bin/bwa [05:04:54] Found bcftools - /usr/local/bin/bcftools [05:04:54] Found samtools - /usr/local/bin/samtools [05:04:54] Found java - /usr/local/bin/java [05:04:55] Found snpEff - /usr/local/bin/snpEff [05:04:55] Found samclip - /usr/local/bin/samclip [05:04:55] Found seqtk - /usr/local/bin/seqtk [05:04:55] Found parallel - /usr/local/bin/parallel [05:04:55] Found freebayes - /usr/local/bin/freebayes [05:04:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:04:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:04:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:04:55] Found vcfuniq - /usr/local/bin/vcfuniq [05:04:55] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:04:55] Found gzip - /bin/gzip [05:04:55] Found vt - /usr/local/bin/vt [05:04:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:04:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:04:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:04:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:04:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:04:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:04:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:04:56] Please supply a reference FASTA/GBK/EMBL file with --reference
1[05:37:33] This is snippy 4.6.0
Show full stderr[05:37:33] This is snippy 4.6.0 [05:37:33] Written by Torsten Seemann [05:37:33] Obtained from https://github.com/tseemann/snippy [05:37:33] Detected operating system: linux [05:37:33] Enabling bundled linux tools. [05:37:33] Found bwa - /usr/local/bin/bwa [05:37:33] Found bcftools - /usr/local/bin/bcftools [05:37:33] Found samtools - /usr/local/bin/samtools [05:37:33] Found java - /usr/local/bin/java [05:37:33] Found snpEff - /usr/local/bin/snpEff [05:37:33] Found samclip - /usr/local/bin/samclip [05:37:33] Found seqtk - /usr/local/bin/seqtk [05:37:33] Found parallel - /usr/local/bin/parallel [05:37:33] Found freebayes - /usr/local/bin/freebayes [05:37:33] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [05:37:33] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [05:37:33] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [05:37:33] Found vcfuniq - /usr/local/bin/vcfuniq [05:37:33] Found vcffirstheader - /usr/local/bin/vcffirstheader [05:37:33] Found gzip - /bin/gzip [05:37:33] Found vt - /usr/local/bin/vt [05:37:33] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [05:37:33] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [05:37:33] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [05:37:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [05:37:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [05:37:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [05:37:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [05:37:34] Please supply a reference FASTA/GBK/EMBL file with --reference
1[07:44:32] This is snippy 4.6.0
Show full stderr[07:44:32] This is snippy 4.6.0 [07:44:32] Written by Torsten Seemann [07:44:32] Obtained from https://github.com/tseemann/snippy [07:44:32] Detected operating system: linux [07:44:32] Enabling bundled linux tools. [07:44:32] Found bwa - /usr/local/bin/bwa [07:44:32] Found bcftools - /usr/local/bin/bcftools [07:44:32] Found samtools - /usr/local/bin/samtools [07:44:32] Found java - /usr/local/bin/java [07:44:32] Found snpEff - /usr/local/bin/snpEff [07:44:32] Found samclip - /usr/local/bin/samclip [07:44:32] Found seqtk - /usr/local/bin/seqtk [07:44:32] Found parallel - /usr/local/bin/parallel [07:44:32] Found freebayes - /usr/local/bin/freebayes [07:44:32] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [07:44:32] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [07:44:32] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [07:44:32] Found vcfuniq - /usr/local/bin/vcfuniq [07:44:32] Found vcffirstheader - /usr/local/bin/vcffirstheader [07:44:32] Found gzip - /bin/gzip [07:44:32] Found vt - /usr/local/bin/vt [07:44:32] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [07:44:32] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [07:44:32] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [07:44:32] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [07:44:32] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [07:44:33] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [07:44:33] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [07:44:33] Please supply a reference FASTA/GBK/EMBL file with --reference
1[23:17:57] This is snippy 4.6.0
Show full stderr[23:17:57] This is snippy 4.6.0 [23:17:57] Written by Torsten Seemann [23:17:57] Obtained from https://github.com/tseemann/snippy [23:17:57] Detected operating system: linux [23:17:57] Enabling bundled linux tools. [23:17:57] Found bwa - /usr/local/bin/bwa [23:17:57] Found bcftools - /usr/local/bin/bcftools [23:17:57] Found samtools - /usr/local/bin/samtools [23:17:57] Found java - /usr/local/bin/java [23:17:57] Found snpEff - /usr/local/bin/snpEff [23:17:57] Found samclip - /usr/local/bin/samclip [23:17:57] Found seqtk - /usr/local/bin/seqtk [23:17:57] Found parallel - /usr/local/bin/parallel [23:17:57] Found freebayes - /usr/local/bin/freebayes [23:17:57] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [23:17:57] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [23:17:57] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [23:17:57] Found vcfuniq - /usr/local/bin/vcfuniq [23:17:57] Found vcffirstheader - /usr/local/bin/vcffirstheader [23:17:57] Found gzip - /bin/gzip [23:17:57] Found vt - /usr/local/bin/vt [23:17:57] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [23:17:57] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [23:17:57] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [23:17:57] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [23:17:57] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [23:17:58] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [23:17:58] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [23:17:58] Please supply a reference FASTA/GBK/EMBL file with --reference
1[02:33:06] This is snippy 4.6.0
Show full stderr[02:33:06] This is snippy 4.6.0 [02:33:06] Written by Torsten Seemann [02:33:06] Obtained from https://github.com/tseemann/snippy [02:33:06] Detected operating system: linux [02:33:06] Enabling bundled linux tools. [02:33:06] Found bwa - /usr/local/bin/bwa [02:33:06] Found bcftools - /usr/local/bin/bcftools [02:33:06] Found samtools - /usr/local/bin/samtools [02:33:06] Found java - /usr/local/bin/java [02:33:06] Found snpEff - /usr/local/bin/snpEff [02:33:06] Found samclip - /usr/local/bin/samclip [02:33:06] Found seqtk - /usr/local/bin/seqtk [02:33:06] Found parallel - /usr/local/bin/parallel [02:33:06] Found freebayes - /usr/local/bin/freebayes [02:33:06] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [02:33:06] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [02:33:06] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [02:33:06] Found vcfuniq - /usr/local/bin/vcfuniq [02:33:06] Found vcffirstheader - /usr/local/bin/vcffirstheader [02:33:06] Found gzip - /bin/gzip [02:33:06] Found vt - /usr/local/bin/vt [02:33:06] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [02:33:06] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [02:33:06] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [02:33:06] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [02:33:06] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [02:33:07] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [02:33:07] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [02:33:07] Please supply a reference FASTA/GBK/EMBL file with --reference
1[02:45:55] This is snippy 4.6.0
Show full stderr[02:45:55] This is snippy 4.6.0 [02:45:55] Written by Torsten Seemann [02:45:55] Obtained from https://github.com/tseemann/snippy [02:45:55] Detected operating system: linux [02:45:55] Enabling bundled linux tools. [02:45:55] Found bwa - /usr/local/bin/bwa [02:45:55] Found bcftools - /usr/local/bin/bcftools [02:45:55] Found samtools - /usr/local/bin/samtools [02:45:55] Found java - /usr/local/bin/java [02:45:55] Found snpEff - /usr/local/bin/snpEff [02:45:55] Found samclip - /usr/local/bin/samclip [02:45:55] Found seqtk - /usr/local/bin/seqtk [02:45:55] Found parallel - /usr/local/bin/parallel [02:45:55] Found freebayes - /usr/local/bin/freebayes [02:45:55] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [02:45:55] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [02:45:55] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [02:45:55] Found vcfuniq - /usr/local/bin/vcfuniq [02:45:55] Found vcffirstheader - /usr/local/bin/vcffirstheader [02:45:55] Found gzip - /bin/gzip [02:45:55] Found vt - /usr/local/bin/vt [02:45:55] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [02:45:55] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [02:45:55] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [02:45:55] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [02:45:55] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [02:45:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [02:45:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [02:45:56] Please supply a reference FASTA/GBK/EMBL file with --reference
1[03:28:39] This is snippy 4.6.0
Show full stderr[03:28:39] This is snippy 4.6.0 [03:28:39] Written by Torsten Seemann [03:28:39] Obtained from https://github.com/tseemann/snippy [03:28:39] Detected operating system: linux [03:28:39] Enabling bundled linux tools. [03:28:39] Found bwa - /usr/local/bin/bwa [03:28:39] Found bcftools - /usr/local/bin/bcftools [03:28:39] Found samtools - /usr/local/bin/samtools [03:28:39] Found java - /usr/local/bin/java [03:28:39] Found snpEff - /usr/local/bin/snpEff [03:28:39] Found samclip - /usr/local/bin/samclip [03:28:39] Found seqtk - /usr/local/bin/seqtk [03:28:39] Found parallel - /usr/local/bin/parallel [03:28:39] Found freebayes - /usr/local/bin/freebayes [03:28:39] Found freebayes-parallel - /usr/local/bin/freebayes-parallel [03:28:39] Found fasta_generate_regions.py - /usr/local/bin/fasta_generate_regions.py [03:28:39] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [03:28:39] Found vcfuniq - /usr/local/bin/vcfuniq [03:28:39] Found vcffirstheader - /usr/local/bin/vcffirstheader [03:28:39] Found gzip - /bin/gzip [03:28:39] Found vt - /usr/local/bin/vt [03:28:39] Found snippy-vcf_to_tab - /usr/local/bin/snippy-vcf_to_tab [03:28:39] Found snippy-vcf_report - /usr/local/bin/snippy-vcf_report [03:28:39] Checking version: samtools --version is >= 1.7 - ok, have 1.13 [03:28:39] Checking version: bcftools --version is >= 1.7 - ok, have 1.13 [03:28:39] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [03:28:40] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [03:28:40] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [03:28:40] Please supply a reference FASTA/GBK/EMBL file with --reference